Resource Type:
Polypeptide
Name:
DCAR_001020
Identifier:
DCAR_001020.mRNA-protein
Sequence:
MFRRSVLGIKQISRIPTRAQTQIPSYLFARKDFSAASKNNASGESGAPSD
PSGSGSNMSKAVIGSLALGFAGIAAYQTGYLDRFLVNEQHNTYDDKSGSG
DQHRQVSTEQGQNTETAESLKDTIDVNTSSKSKDSSNSQAALPPGSSQPD
VSPISDYKLASSAQSSEATDPGSTNNVTQDEKNHHSKSPDVNPGEQHEPV
DTTVVVTHANEVPKEVELNKPTQQTHITALEDNKGNSKEQSIALLNEYHL
LDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKR
QAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKV
KAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASE
KASQIEKMAEADLNINALHTYLEGIEKDSLLDVVLSSFPEETRTGGTDTL
LQLNQKFDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDG
IESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAIT
EQSLTFLHSYATAASLS*
Sequence Length:
568
Sequence Checksum:
81e72a889f8b42911ab5c0e726dc2875
View location in JBrowse:
Organism:
Relationship:
| Relationships |
|---|
| The polypeptide, DCAR_001020, derives from mRNA, DCAR_001020. |
Blast Results:
The following BLAST results are available for this feature:
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5B7A9C7 ((Uncharacterized protein {ECO:0000313|EMBL:MPA53339.1}))
HSP 1 Score: 586.26 bits (1510), Expect = 0.000e+0
Identity = 355/650 (54.62%), Postives = 435/650 (66.92%), Query Frame = 0
Match: A0A5B7A9C7 ((Uncharacterized protein {ECO:0000313|EMBL:MPA53339.1}))
HSP 1 Score: 586.26 bits (1510), Expect = 0.000e+0
Identity = 355/650 (54.62%), Postives = 435/650 (66.92%), Query Frame = 0
Query: 1 MFRRSVLGI---KQISRIPTRAQTQIPSYLFARKDFSAASKNNASGESGAPSDPSGSGSNMSKAVIGSLALGFAGIAAYQTGYLDRFLVNEQHNTYDD-KSGSGDQHRQVSTEQGQNTETAESLKDTIDVNTSSKSKDSS----------NSQAALP--------PGSSQPDVSPISDYK--------------LASSAQSSEATDPGSTNNVTQDEKNHHSKSPDVNPG-EQHEPVDTTVVVTHANEVPKEVEL-NKPTQQTHITAL-EDNKGNSKEQSIALLNEYHLLDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKRQAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKVKAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASEKASQIEKMAEADLNINAL--------------------------------------------HTYLEGIEKDSLLDVVLSSFPEETRTGGTDTLLQLNQKFDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDGIESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAITEQSLTFLHSYATAASLS 567
M RRS+L + + + RIPTR TQIP YL +RK+FS AS+ NA SG+ +P+ SGS +SK VIGS+ALG A + AYQTGYLD+ LV EQH+ + K+ S ++ S +++E + L++ + +SK SS ++ + LP G SQ V +S+ + L SS QSS +D STN T E++ KSP++ P EQ V+ T ++T AN +PKE E+ + P Q L ED N EQ +LL+ Y+L DK EETSATS E KD G ++D DVH++KDG+L+LDFLQAIHAAEKRQA LDA F EEKRI+KEKYEKEL+DA A+ELMYAE A+LDK+LNKE+VKAAAALKSL+EKLEE+ + ELEQKEAEA L+LKK +EL KAELASAIASEKASQIEKM EA+L+INAL H YLEGI+KDSLLD+VLSS PEETR GTDTLLQLN KFDALKGTLRHFSLIPPGGGGIL HSLA VASLLKV+E D+SGDGIESLINRVESFLA+GKL EAADTLEDG+KGS+A+ +V DWV++ARNRAITEQ+LT L SYAT+ SL+
Sbjct: 1 MLRRSILELSSRQSVRRIPTRITTQIPLYLSSRKEFSVASQQNAPKGSGSTGNPTDSGSYLSKIVIGSVALGAAVMTAYQTGYLDKVLVKEQHSALESAKTDSVNKDSLESLRSNEDSEDDKRLREQTVMPNIQESKVSSPNVEHAEKNTDTHSFLPHLEDSSRSEGESQFHVKDVSELRHEDDITPMQEKEKELPSSPQSSMTSDDESTNARTPLEESPEMKSPEMKPRIEQQGAVEITPIITQANAIPKENEMKSMPPQDLTTKYLPEDASVNGLEQPSSLLDAYYLRDKAEETSATSSNEHKDSIGVIEDMNDVHISKDGKLVLDFLQAIHAAEKRQAELDAHIFAEEKRIVKEKYEKELKDARAKELMYAEEVAMLDKDLNKERVKAAAALKSLQEKLEEKREMELEQKEAEAELKLKKIQELAKAELASAIASEKASQIEKMTEANLHINALCMAFYAQSKEARQSHSVHKLALGALALEDALSKGLPIQKEIDALHIYLEGIDKDSLLDLVLSSLPEETRKYGTDTLLQLNHKFDALKGTLRHFSLIPPGGGGILAHSLAHVASLLKVREVDQSGDGIESLINRVESFLAEGKLSEAADTLEDGVKGSQATEIVGDWVRQARNRAITEQALTLLQSYATSISLT 650
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5B7A9L1 ((Uncharacterized protein {ECO:0000313|EMBL:MPA53337.1}))
HSP 1 Score: 579.326 bits (1492), Expect = 0.000e+0
Identity = 353/650 (54.31%), Postives = 432/650 (66.46%), Query Frame = 0
Match: A0A5B7A9L1 ((Uncharacterized protein {ECO:0000313|EMBL:MPA53337.1}))
HSP 1 Score: 579.326 bits (1492), Expect = 0.000e+0
Identity = 353/650 (54.31%), Postives = 432/650 (66.46%), Query Frame = 0
Query: 1 MFRRSVLGI---KQISRIPTRAQTQIPSYLFARKDFSAASKNNASGESGAPSDPSGSGSNMSKAVIGSLALGFAGIAAYQTGYLDRFLVNEQHNTYDD-KSGSGDQHRQVSTEQGQNTETAESLKDTIDVNTSSKSKDSS----------NSQAALP--------PGSSQPDVSPISDYK--------------LASSAQSSEATDPGSTNNVTQDEKNHHSKSPDVNPG-EQHEPVDTTVVVTHANEVPKEVEL-NKPTQQTHITAL-EDNKGNSKEQSIALLNEYHLLDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKRQAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKVKAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASEKASQIEKMAEADLNINAL--------------------------------------------HTYLEGIEKDSLLDVVLSSFPEETRTGGTDTLLQLNQKFDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDGIESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAITEQSLTFLHSYATAASLS 567
M RRS+L + + + RIPTR TQIP YL +RK+FS AS+ NA SG+ +P+ SGS +SK VIGS+ALG A + AYQTGYLD+ LV EQH+ + K+ S ++ S +++E + L++ + +SK SS ++ + LP G SQ V +S+ + L SS QSS +D STN T E++ KSP++ P EQ V+ T ++T AN +PKE E+ + P Q L ED N EQ +LL+ Y+L DK EETSATS E KD G ++D DVH++KDG+L+LDFLQAIHAAEKRQA LDA F EEKRI+KEKYEKEL+DA A+ELMYAE A+LDK+LNKE+VKAAAALKSL+EKLEE+ + ELEQKEAEA L+LKK +EL KAELASAIASEKASQIEKM EA+L+INAL H YLEGI+KDSLLD+VLSS PEETR GTDTLLQLN KFDALKGTLRHFSLIPPGGGGIL HSLA VASLLKV+E D+SGDGIESLINRVESFLA+GKL EAADTLE+ +KGS+A+ +V DWV ARNRAITEQ+LT L SYAT+ SL+
Sbjct: 1 MLRRSILELSSRQSVRRIPTRITTQIPLYLSSRKEFSVASQQNAPKGSGSTGNPTDSGSYLSKIVIGSVALGAAVMTAYQTGYLDKVLVKEQHSALESAKTDSVNKDSLESLRSNEDSEDDKRLREQTVMPNIQESKVSSPNVEHAEKNTDTHSFLPHLEDSSRSEGESQFHVKDVSELRHEDDITPMQEKEKELPSSPQSSMTSDDESTNARTPLEESPEMKSPEMKPRIEQQGAVEITPIITQANAIPKENEMKSMPPQDLTTKYLPEDASVNGLEQPSSLLDAYYLRDKAEETSATSSNEHKDSIGVIEDMNDVHISKDGKLVLDFLQAIHAAEKRQAELDAHIFAEEKRIVKEKYEKELKDARAKELMYAEEVAMLDKDLNKERVKAAAALKSLQEKLEEKREMELEQKEAEAELKLKKIQELAKAELASAIASEKASQIEKMTEANLHINALCMAFYAQSKEARQSHSVHKLALGALALEDALSKGLPIQKEIDALHIYLEGIDKDSLLDLVLSSLPEETRKYGTDTLLQLNHKFDALKGTLRHFSLIPPGGGGILAHSLAHVASLLKVREVDQSGDGIESLINRVESFLAEGKLSEAADTLEESVKGSQAAEIVGDWVWCARNRAITEQALTLLQSYATSISLA 650
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5B7ABR8 ((Putative MICOS complex subunit MIC60 isoform X1 {ECO:0000313|EMBL:MPA53338.1}))
HSP 1 Score: 572.007 bits (1473), Expect = 0.000e+0
Identity = 350/647 (54.10%), Postives = 429/647 (66.31%), Query Frame = 0
Match: A0A5B7ABR8 ((Putative MICOS complex subunit MIC60 isoform X1 {ECO:0000313|EMBL:MPA53338.1}))
HSP 1 Score: 572.007 bits (1473), Expect = 0.000e+0
Identity = 350/647 (54.10%), Postives = 429/647 (66.31%), Query Frame = 0
Query: 4 RSVLGI---KQISRIPTRAQTQIPSYLFARKDFSAASKNNASGESGAPSDPSGSGSNMSKAVIGSLALGFAGIAAYQTGYLDRFLVNEQHNTYDD-KSGSGDQHRQVSTEQGQNTETAESLKDTIDVNTSSKSKDSS----------NSQAALP--------PGSSQPDVSPISDYK--------------LASSAQSSEATDPGSTNNVTQDEKNHHSKSPDVNPG-EQHEPVDTTVVVTHANEVPKEVEL-NKPTQQTHITAL-EDNKGNSKEQSIALLNEYHLLDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKRQAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKVKAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASEKASQIEKMAEADLNINAL--------------------------------------------HTYLEGIEKDSLLDVVLSSFPEETRTGGTDTLLQLNQKFDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDGIESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAITEQSLTFLHSYATAASLS 567
RS+L + + + RIPTR TQIP YL +RK+FS AS+ NA SG+ +P+ SGS +SK VIGS+ALG A + AYQTGYLD+ LV EQH+ + K+ S ++ S +++E + L++ + +SK SS ++ + LP G SQ V +S+ + L SS QSS +D STN T E++ KSP++ P EQ V+ T ++T AN +PKE E+ + P Q L ED N EQ +LL+ Y+L DK EETSATS E KD G ++D DVH++KDG+L+LDFLQAIHAAEKRQA LDA F EEKRI+KEKYEKEL+DA A+ELMYAE A+LDK+LNKE+VKAAAALKSL+EKLEE+ + ELEQKEAEA L+LKK +EL KAELASAIASEKASQIEKM EA+L+INAL H YLEGI+KDSLLD+VLSS PEETR GTDTLLQLN KFDALKGTLRHFSLIPPGGGGIL HSLA VAS LKV+E D+SGDGIESLINRVESFLA+GKL EAADTLE+ +KGS+A+ +V DWV ARNRAITEQ+LT L SYAT+ SL+
Sbjct: 27 RSILELSSRQSVRRIPTRITTQIPLYLSSRKEFSVASQQNAPKGSGSTGNPTDSGSYLSKIVIGSVALGAAVMTAYQTGYLDKVLVKEQHSALESAKTDSVNKDSLESLRSNEDSEDDKRLREQTVMPNIQESKVSSPNVEHAEKNTDTHSFLPHLEDSSRSEGESQFHVKDVSELRHEDDITPMQEKEKELPSSPQSSMTSDDESTNARTPLEESPEMKSPEMKPRIEQQGAVEITPIITQANAIPKENEMKSMPPQDLTTKYLPEDASVNGLEQPSSLLDAYYLRDKAEETSATSSNEHKDSIGVIEDMNDVHISKDGKLVLDFLQAIHAAEKRQAELDAHIFAEEKRIVKEKYEKELKDARAKELMYAEEVAMLDKDLNKERVKAAAALKSLQEKLEEKREMELEQKEAEAELKLKKIQELAKAELASAIASEKASQIEKMTEANLHINALCMAFYAQSKEARQSHSVHKLALGALALEDALSKGLPIQKEIDALHIYLEGIDKDSLLDLVLSSLPEETRKYGTDTLLQLNHKFDALKGTLRHFSLIPPGGGGILAHSLAHVASWLKVREVDQSGDGIESLINRVESFLAEGKLSEAADTLEESVKGSQAAEIVGDWVWCARNRAITEQALTLLQSYATSISLA 673
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6I9U964 ((MICOS complex subunit Mic60 {ECO:0000313|RefSeq:XP_011090456.1}))
HSP 1 Score: 503.056 bits (1294), Expect = 7.370e-170
Identity = 311/657 (47.34%), Postives = 408/657 (62.10%), Query Frame = 0
Match: A0A6I9U964 ((MICOS complex subunit Mic60 {ECO:0000313|RefSeq:XP_011090456.1}))
HSP 1 Score: 503.056 bits (1294), Expect = 7.370e-170
Identity = 311/657 (47.34%), Postives = 408/657 (62.10%), Query Frame = 0
Query: 1 MFRRSVLGI---KQISRIPTRAQTQIPSYLFARKDFSAASKNNASGESGAPSDP-SGSG-----SNMSKAVIGSLALGFAGIAAYQTGYLDRFLVNEQHNT--YDDKSGSGDQHRQVSTEQGQNTETAESLKDTIDVNTSSKSKDS------------SNSQAALPPGS-----------------SQPDVSPISDYKLASSAQSSEATDPGSTNNVTQDEKNHHSKSPDVNPG-EQHEPVDTTVVVTHANEVPKEVELNK----PTQQTHITALEDN-KGNSKEQSIALLNEYHLLDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKRQAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKVKAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASEKASQIEKMAEADLNINAL--------------------------------------------HTYLEGIEKDSLLDVVLSSFPEETRTGGTDTLLQLNQKFDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDGIESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAITEQSLTFLHSYATAASLS 567
MFRRS+L + +SR+P R TQIPSYL R+ F + KN P P SG G S + K + G LALG +AAY G LDR++ EQ + Y + + +GD++ + EQ A L + N+ S S +++Q +P S + +V + L ++ QSS +D ++ E++ KSP V P EQ++ ++T + T A++ P E++ PT+QT +++ K +S ++S +LL++Y+L DK+EE+ +S ++LKD+ ++D D +TKDG+L+LDFLQAIHAAE+RQA LDA F EEK+ MKEKYEKEL+DA RELMYAEREAILDKELNKE+VKAAAALKSL+EKLEE+LK ELEQKE E +LK+ +++ KAELA+AIA EKASQIEKMAEA+L+INAL HT++EGI+ DSL+ +VLSS P++T+ GTDTL QLN KFD LKG LRHFSLIPPGGGGIL HSLA VAS LKVKE D SGDGIES+INRVES LA GKL EAADTLE+G+KGS+A+ VV DWV++ARNRAITEQ+LT L SYAT+ SL+
Sbjct: 1 MFRRSILQLASRSSVSRVPLRTTTQIPSYLSFRRAFCVSPKNE-------PIKPDSGGGAPEPESRLPKVLAGGLALGSVFLAAYYYGALDRYVGKEQQSMSKYTN-AWTGDKNTETPPEQQNAYLQARELSEAAAGNSPQGSDVSISDADHARQDVQTHAQLNVPEESIKTGEDKGHQAKDMAVLAPENVDHVEGRDLPTAPQSSMPSDDVTSKPA---EQSFDLKSPQVKPDDEQNKATESTPIFTAADKTPAEIDTKPVSPVPTEQTTTQDMQEAVKDDSIQKSSSLLDDYYLRDKSEESVTSSSSKLKDISSSMEDVYDGFITKDGKLVLDFLQAIHAAEERQAELDAHFFAEEKKAMKEKYEKELKDARVRELMYAEREAILDKELNKERVKAAAALKSLQEKLEEKLKTELEQKEMEVEQKLKQMQDMSKAELAAAIAREKASQIEKMAEANLHINALCMAFYARSEEVRQTHSVHKLALGALALEDALGKGLPIKKEIEALHTHVEGIDDDSLIALVLSSLPDDTQKYGTDTLSQLNHKFDVLKGMLRHFSLIPPGGGGILTHSLAHVASWLKVKEVDHSGDGIESIINRVESLLAQGKLCEAADTLENGVKGSQAAEVVNDWVKRARNRAITEQALTILQSYATSISLT 646
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A2R6PAU2 ((MICOS complex subunit mic60 like {ECO:0000313|EMBL:PSR88101.1}))
HSP 1 Score: 501.901 bits (1291), Expect = 1.858e-169
Identity = 306/654 (46.79%), Postives = 410/654 (62.69%), Query Frame = 0
Match: A0A2R6PAU2 ((MICOS complex subunit mic60 like {ECO:0000313|EMBL:PSR88101.1}))
HSP 1 Score: 501.901 bits (1291), Expect = 1.858e-169
Identity = 306/654 (46.79%), Postives = 410/654 (62.69%), Query Frame = 0
Query: 1 MFRRSVLGI---KQISRIPTRAQTQIPSYLFARKDFSAASKNNASGESGAPSDPSGSGSNMSKAVIGSLALGFAGIAAYQTGYLDRFLVNEQHNTYDD-KSGS-------------------GDQHRQVSTEQG-----------QNTETAESLKDTIDVNTSSKSKDSSNSQAALPPGS---SQPDVSPISDYKLASSAQ---SSEATDPGSTNNVTQDEKNHHSKSPDVNPGE-QHEPVDTTVVVTHANEVPKEVELNKPT--QQTHITALEDNKGNSKEQSIALLNEYHLLDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKRQAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKVKAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASEKASQIEKMAEADLNINAL--------------------------------------------HTYLEGIEKDSLLDVVLSSFPEETRTGGTDTLLQLNQKFDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDGIESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAITEQSLTFLHSYATAASLS 567
M RRS+L + + +R PTR TQIPSYL RK +S +S+ N SG+ P SGS++ K VIGSL LG A + AY +L++ V E+ + + K+G+ G+Q+ + E+ +N ET L D+ ++ SQ + + ++ D++PI +L+ S Q +S+ T P T+ E+ ++S +V P Q E ++T +++ AN + +E E+ + QQT I ED NS E+ +LL+EY+L DK +ET +T + KDL G ++S+DV ++KDG+L++DFLQAIH AEKRQA LDA F EEKR +KEKYEKEL+DA ARELMYAE AILDKELN+E+VKAAAALKSL E+LE +L+ ELEQK AEA L LKK +EL AEL +AIASEKASQIEKMAEA+L+I+AL ++YL+ I KD LD+VLSS PEE R+ GTDT+LQL +FDALKGTLR FSL+PPGGGGIL +SLA +ASLLKV+EAD+SGDGIESL+NRVESFLA+GKL EAAD LE+G+KG++A+ V+ DW+++ RNRAITEQ+LT L SYAT+ SL+
Sbjct: 1 MLRRSILELSSRRSFTRNPTRITTQIPSYLSCRKQYSVSSEQNVPQGSGSTGKPPESGSSLPKIVIGSLTLGAALMTAY---HLNQRFVEERRSAVESSKTGTKDSVNLSISVKELQEDKHLGEQNVMSNIEESNVSSLNMEPAEENIETHSGLPHLDDLR-----RNEEESQLQVKDKTQLTTEEDIAPIQVKELSGSPQINVTSDETKPSGTSL----EEMADARSTEVKPNMVQQEAYESTPILSQANSILEENEMKSTSIQQQTAIDTKEDAHCNSGERPNSLLDEYYLKDKVQETISTLSDKHKDLVGATEESSDV-ISKDGKLVIDFLQAIHTAEKRQAELDAHIFAEEKRKIKEKYEKELKDARARELMYAEEAAILDKELNRERVKAAAALKSLREELEGKLRMELEQKGAEAELNLKKIQELAIAELTAAIASEKASQIEKMAEANLHIDALCMAFFARSEEARQSHSAHKLALGALALEDALSKGLPIQKEIDALYSYLKDIYKDPFLDLVLSSLPEEARSSGTDTVLQLKHQFDALKGTLRRFSLMPPGGGGILAYSLAHIASLLKVREADQSGDGIESLMNRVESFLAEGKLSEAADALENGVKGTQAAEVIGDWLRQVRNRAITEQALTLLQSYATSVSLT 641
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6P6TKX8 ((MICOS complex subunit MIC60-like {ECO:0000313|RefSeq:XP_027079173.1}))
HSP 1 Score: 495.352 bits (1274), Expect = 6.217e-167
Identity = 304/651 (46.70%), Postives = 401/651 (61.60%), Query Frame = 0
Match: A0A6P6TKX8 ((MICOS complex subunit MIC60-like {ECO:0000313|RefSeq:XP_027079173.1}))
HSP 1 Score: 495.352 bits (1274), Expect = 6.217e-167
Identity = 304/651 (46.70%), Postives = 401/651 (61.60%), Query Frame = 0
Query: 1 MFRRSVLGIKQI---SRIPTRAQTQIPSYLFARKDFSAASKNNASGESGAPSDPSGSGSNMSKAVIGSLALGFAGIAAYQTGYLDRFLVNEQHNTYDDKSGSGDQHRQVSTEQGQNTE-TAESLKDTIDVNTS----------------------------------SKSKDSSNSQAALPPGSSQPDVSPISDYKLASSAQSSEATDPGSTNNVTQDEKNHHSKSPDVN-PGEQHEPVDTTVVVTHANEVPKEVELNK-PTQQTHITALEDNKGNSKEQSIALLNEYHLLDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKRQAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKVKAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASEKASQIEKMAEADLNINAL--------------------------------------------HTYLEGIEKDSLLDVVLSSFPEETRTGGTDTLLQLNQKFDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDGIESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAITEQSLTFLHSYATAASLS 567
M RRS+L + RIP + +QIPSYL +R+ SAAS++N G+ +D + SGS++ K ++G +ALG + AY TGYLDRF E H T + + VS EQ E + +SL D + T S+ ++ S+ P D++ I + +L SS S +D S N E + S DV +Q + V+ T T ++ E E N P Q + ++N ++ Q+ +LL++Y+L E + S ++ + L G +++S ++++DG+L++DFLQAIHAAEKRQA LDA F E+K ++KEKYEKELRDA ARELMYAEREAIL+KELNKE+VKAAAALKSL+EKLEE+ K ELE K+ EA LE+KK +EL KAELASAIASEKA+QIEKMAEA+++INAL HTY+EGI+KDSLLD+VLSS PEETR GTDT+LQLN KFDAL+GTLR +SLIP GGGGIL HSLA VAS LKV+EAD+SGDGIESL+NRV+SFLA+GKL EAAD LE+G+KG++A+ VV DWV++ARNRA+TEQ+LT L SYAT+ SL+
Sbjct: 1 MLRRSILRLSSCRLDGRIPIQITSQIPSYLSSRRAMSAASQHNEPQGPGS-ADKAESGSSLPKILVGGVALGAVVMGAYHTGYLDRFFAKEPHGTAESAKVAA-----VSEEQPDLREDSKKSLVDEDKIETIANLKYEQTSIPTPKMEHEEKSMSSDSDPSPREDLSRRQEESHFHMKDKPDLKSDDINHIQEEELPSSLGSGTQSDDLSANLGKPSEGSLTMNSSDVKVDSDQQKAVEMTPPFTRDDKAAAENETNSVPVQFNSQDSPKENLAGARRQTSSLLDDYNLKSDGNEPTLVSTSKSQGLPGTIEES---YISEDGKLVIDFLQAIHAAEKRQAELDAHTFAEDKIMLKEKYEKELRDARARELMYAEREAILNKELNKERVKAAAALKSLQEKLEEKHKMELEIKKNEAELEMKKLQELAKAELASAIASEKAAQIEKMAEANVHINALCMAFYARSEEARQSHSVHKLALGALALEDALTKGLPIQKEMEALHTYVEGIDKDSLLDLVLSSIPEETRINGTDTVLQLNHKFDALRGTLRRYSLIPLGGGGILAHSLAHVASWLKVREADQSGDGIESLMNRVDSFLAEGKLSEAADALENGVKGTQAAEVVGDWVRRARNRAVTEQALTLLQSYATSISLT 642
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A103XAZ9 ((Mitochondrial inner membrane protein Mitofilin {ECO:0000313|EMBL:KVH87393.1}))
HSP 1 Score: 491.886 bits (1265), Expect = 6.785e-166
Identity = 292/589 (49.58%), Postives = 381/589 (64.69%), Query Frame = 0
Match: A0A103XAZ9 ((Mitochondrial inner membrane protein Mitofilin {ECO:0000313|EMBL:KVH87393.1}))
HSP 1 Score: 491.886 bits (1265), Expect = 6.785e-166
Identity = 292/589 (49.58%), Postives = 381/589 (64.69%), Query Frame = 0
Query: 23 IPSYLFARKDFSAASKNNASGESGAPSDPSGSGSNMSKAVIGSLALGFAGIAAYQTGYLDRFLVNEQHNTYD-------------DKSGSGDQH-----RQVSTEQGQNTE----TAESLKDTIDVNTS-SKSKDSSNSQAALPPGSSQPDVSPISDYKLASSAQSSEATDPGSTNNVTQDEKNHHSKSPDVNPG-EQHEPVDTTVVVTHANEVPKE--VELNKPTQQTHITALEDNKGNSKEQSIALLNEYHLLDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKRQAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKVKAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASEKASQIEKMAEADLN------------------INALHTYLEGIEKDSLLDVVLSSFPEETRTGGTDTLLQLNQKFDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDGIESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAITEQSLTFLHSYATAASLS 567
IP YLF+RK+FS A ++N+S SG+ P SGSN+SK IGSLA+G A + AYQTGYL+ FL EQ+N + K+ +GD H V+ + Q +E T E + I ++ S+ ++ + S+ P S D + KL S S S +++ +++ +K+ DV P E+HE V T + T V +E ++ +P Q I E N ++ +LL+ Y L K E+T+A S KD+ VK + DV+V+KDG+++LD L+AIH AE+RQ EKYEKEL+DA ARELMYAERE ILDKEL+KEK+KAAAALKSL+E LEE+ + E+E+KE+E EL K ++L KAEL + IASEKASQIE+M EA+LN I+AL++Y++GI+KDSLL +V++S PE+T GTDT+LQLN KFD LKGTLRHFSL+PPGGGGIL HSLA +AS LKVKEAD+SGDGIESLINRVES LADGKLLEAA+TLEDGLKGS+A+ VV DWVQ+ARNRAITEQ+LT L SYAT+ SLS
Sbjct: 42 IPLYLFSRKEFSVAPQSNSSKPSGSTGKPPDSGSNLSKVFIGSLAIGAAALTAYQTGYLETFLTKEQNNDLNTHEIPIVHEEPQQPKTVNGDLHDGETVEPVAVQNVQESEVSNPTVEHGEKNIHIDPYYSRREEEAQSELKELPISKPHDAISEQESKLPSLDHSISTAHDSSFDSIPLIQEDLGTKNQDVKPTIERHEGVQITSIPTQVAPVIEENMIKSEQPQQLGTINMPERILSNDVKEPNSLLDAYLLRGKAEQTAAASSYLHKDIAETVKGTNDVYVSKDGKVVLDLLEAIHTAERRQ----------------EKYEKELKDARARELMYAERETILDKELHKEKLKAAAALKSLQEMLEEEFRMEIERKESETEFELNKLKDLAKAELTAGIASEKASQIERMEEANLNGALALEDALSKGLPIQKEIDALNSYIDGIDKDSLLGLVMASLPEDTLKNGTDTILQLNHKFDGLKGTLRHFSLMPPGGGGILAHSLAYIASNLKVKEADKSGDGIESLINRVESLLADGKLLEAAETLEDGLKGSQAAEVVGDWVQQARNRAITEQALTLLQSYATSVSLS 614
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6P6TBN4 ((MICOS complex subunit MIC60-like {ECO:0000313|RefSeq:XP_027075545.1}))
HSP 1 Score: 491.886 bits (1265), Expect = 1.734e-165
Identity = 300/646 (46.44%), Postives = 398/646 (61.61%), Query Frame = 0
Match: A0A6P6TBN4 ((MICOS complex subunit MIC60-like {ECO:0000313|RefSeq:XP_027075545.1}))
HSP 1 Score: 491.886 bits (1265), Expect = 1.734e-165
Identity = 300/646 (46.44%), Postives = 398/646 (61.61%), Query Frame = 0
Query: 1 MFRRSVLGIKQI---SRIPTRAQTQIPSYLFARKDFSAASKNNASGESGAPSDPSGSGSNMSKAVIGSLALGFAGIAAYQTGYLDRFLVNEQHNTYDDKSGSGDQHRQVSTEQGQN--------TETAESLK-DTIDVNTS---------------------SKSKDSSNSQAALPPGSSQPDVSPISDYKLASSAQSSEATDPGSTNNVTQDEKNHHSKSPDVN-PGEQHEPVDTTVVVTHANEVPKEVELNK-PTQQTHITALEDNKGNSKEQSIALLNEYHLLDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKRQAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKVKAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASEKASQIEKMAEADLNINAL--------------------------------------------HTYLEGIEKDSLLDVVLSSFPEETRTGGTDTLLQLNQKFDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDGIESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAITEQSLTFLHSYATAASLS 567
M RRS+L + RIP + +QIPSYL +R+ SAAS++N G+ +D + S S++ K ++G +ALG + AY TGYLDRF E H T + + Q+ + ET +LK + + T S+ ++ S+ P D++ I + +L SS S +D S N E + S DV +Q + V+ T T + E E N P Q + ++N +++ Q+ +LL++Y+L E + S ++ + L G +++S ++++DG+L++DFLQAIHAAEKRQA LDA F E+K ++KEKYEKELRDA ARELMYAEREAIL+KELNKE+VKAAAALKSL+EKLEE+ K ELE K+ EA LE+KK +EL KAELASAIASEKA+QIEKMAEA+++INAL HTYLEGI+KDSLLD+VLSS PEETR GTDT+LQLN KFDAL+GTLR +SLIP GGGGIL HSLA VAS LKV+EAD+SGDGIESL+NRV+SFLA+GKL EAAD LE+G+KG++A+ VV DWV++ARNRA+ EQ+LT L SYAT+ SL+
Sbjct: 1 MLRRSILRLSSCRLDGRIPIQITSQIPSYLSSRRAMSAASQHNEPQGPGS-ADKAESRSSLPKILVGGVALGAVVMGAYHTGYLDRFFAKEPHGTAESAKVAAVSEEQLDLREDSKKSLVDEDKIETIANLKYEQTSIPTPKMEHEEKSMSSDSDPSPREDLSRRQEESHFHMKDKPDLKSDDINHIQEEELPSSLGSGTQSDDLSANLGKPSEGSLTMNSSDVKVDSDQQKAVEMTPPFTRDDTAAAENETNSVPVQFNSQDSPKENLASARRQTSSLLDDYNLKSDGNEPTLVSTSKSQGLPGTIEES---YISEDGKLVIDFLQAIHAAEKRQAELDAHTFAEDKIMLKEKYEKELRDARARELMYAEREAILNKELNKERVKAAAALKSLQEKLEEKHKMELEIKKNEAELEMKKLQELAKAELASAIASEKAAQIEKMAEANVHINALCMAFYARSEEARQSHSVHKLALGALALEDALTKGLPIQKEMEALHTYLEGIDKDSLLDLVLSSIPEETRINGTDTVLQLNHKFDALRGTLRRYSLIPLGGGGILAHSLAHVASWLKVREADQSGDGIESLMNRVDSFLAEGKLSEAADALENGVKGTQAAEVVGDWVRRARNRAVAEQALTLLQSYATSISLT 642
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5B7AC34 ((Putative MICOS complex subunit MIC60 isoform X1 {ECO:0000313|EMBL:MPA53336.1}))
HSP 1 Score: 481.1 bits (1237), Expect = 4.201e-164
Identity = 278/444 (62.61%), Postives = 327/444 (73.65%), Query Frame = 0
Match: A0A5B7AC34 ((Putative MICOS complex subunit MIC60 isoform X1 {ECO:0000313|EMBL:MPA53336.1}))
HSP 1 Score: 481.1 bits (1237), Expect = 4.201e-164
Identity = 278/444 (62.61%), Postives = 327/444 (73.65%), Query Frame = 0
Query: 169 TDPGSTNNVTQDEKNHHSKSPDV-NPGEQHEPVDTTVVVTHANEVPKEVELNKPTQQTHITALEDNKGNSKEQSIALLNEYHLLDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKRQAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKVKAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASEKASQIEKMAEADLNINAL--------------------------------------------HTYLEGIEKDSLLDVVLSSFPEETRTGGTDTLLQLNQKFDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDGIESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAITEQSLTFLHSYATAASLS 567
+D STN T E++H KS +V + EQHE V+ T +VT+AN +P+E E+ Q H T ED+ N EQ LL+ Y+L DK EETSATS E KD G +++ DV+++KDG+L+LDFLQAIHAAEKRQA LDA F EEKRI+KEKYEKEL+DA A+ELMYAE A+LDK+LNKE+VKAAAALKSL+EKLEE+ + ELEQKEAEA L+LKK +EL KAELASAIASEKASQIEKM EA+L+INAL H YLEGI+KDSLLD+VLSS PEETR GTDTLLQLN KFDALKGTLR FSLIPPGGGGIL HSLA VAS LKV+E D+SGDGIESLINRVESFLA+GKL EAADTLEDG+KGS+A+ +V DWV++ARNRAITEQ+LT L SYAT+ SL+
Sbjct: 3 SDYESTNARTPLEESHDKKSSEVKHRTEQHEAVEITPIVTNANTIPEENEMKSMPPQ-HFTTTEDDSVNGIEQPSFLLDAYYLRDKAEETSATSLNEHKDSVGAIEELNDVYISKDGKLVLDFLQAIHAAEKRQAELDAHIFAEEKRIVKEKYEKELKDARAKELMYAEEVAMLDKDLNKERVKAAAALKSLQEKLEEKREMELEQKEAEAELKLKKIQELAKAELASAIASEKASQIEKMTEANLHINALCMAFYAQSKEARQSHSVHKLALGALALEDALSKGLPIQKEIDALHIYLEGIDKDSLLDLVLSSLPEETRKYGTDTLLQLNHKFDALKGTLRCFSLIPPGGGGILAHSLAHVASWLKVREVDQSGDGIESLINRVESFLAEGKLSEAADTLEDGVKGSQATEIVGDWVRQARNRAITEQALTLLQSYATSISLA 445
BLAST of DCAR_001020 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A834GAT6 ((Uncharacterized protein {ECO:0000313|EMBL:KAF7130054.1}))
HSP 1 Score: 486.108 bits (1250), Expect = 4.568e-163
Identity = 306/660 (46.36%), Postives = 397/660 (60.15%), Query Frame = 0
Match: A0A834GAT6 ((Uncharacterized protein {ECO:0000313|EMBL:KAF7130054.1}))
HSP 1 Score: 486.108 bits (1250), Expect = 4.568e-163
Identity = 306/660 (46.36%), Postives = 397/660 (60.15%), Query Frame = 0
Query: 1 MFRRSVLGI---KQISRIPTR------------AQTQIPSYLFARKDFSAASKNNASGESGAPSDPSGSGSNMSKAVIGSLALGFAGIAAYQT------GYLDRF---------LVNEQHNTYDDKSGSGDQHRQVST---EQGQNTETAESLKDTI---------DVNTSSKSKDSSNSQAALPPGSSQPDVSPISDYKLASSAQSSEATDPGSTNNVTQDEKNHHSKSPDVNPG-EQHEPVDTTVVVTHANEVPKEVELNKPT-QQTHITALEDNKGNSKEQSIALLNEYHLLDKTEETSATSHTELKDLDGEVKDSADVHVTKDGQLILDFLQAIHAAEKRQAALDAQKFGEEKRIMKEKYEKELRDAIARELMYAEREAILDKELNKEKVKAAAALKSLEEKLEEQLKKELEQKEAEAALELKKFEELGKAELASAIASEKASQIEKMAEADLNINAL--------------------------------------------HTYLEGIEKDSLLDVVLSSFPEETRTGGTDTLLQLNQK-----FDALKGTLRHFSLIPPGGGGILVHSLASVASLLKVKEADRSGDGIESLINRVESFLADGKLLEAADTLEDGLKGSEASGVVADWVQKARNRAITEQSLTFLHSYATAASLS 567
M RRS+L I + + R P R +T IP+Y+ RK +S AS+ NA SG+ P SGS++ K +IG+L LG + AY G L F V + D K + + V + E G +T + KD + D++ +S+ N + P + + D +P + +L + E+ PG++ T D K P+V EQHE V+ ++ N V +E E+ + QQ T + + G+ EQ +LLNEY+L DK EET +T + KDL ++DS D +++KDG+L++DFLQAIHAAEKRQA LDA F EEKR MKEKYEKEL+DA ARELMYAE AI+DKELN+E++KA AALKSL E+LE++L+ ELEQKE EA LK +EL KAELA+AIASEKAS IEKMAEA+L+INAL HTYLEG KD LLD+VLSS P+ET++ GTDT+LQL K FD LKGTLRHFSLIPPGGGGIL HSLA VAS LKVKEAD+SGDGIESLINRVES LA+GKL EAAD+LE+G+KG++A+ V+ DW+++ RNRAITEQ+LTF+ +YATA SL+
Sbjct: 1 MLRRSILEISSRQSLRRNPARIAAQACHPISSFGRTNIPAYISCRKQYSVASEQNAPQGSGSTGKPPESGSSLPKIIIGTLTLGAVLMTAYHLNQRSIEGRLSIFESLKVGTKDPVELSKSNKDLKEDGVLRDKNVMSSIQESGGSTNMEPAGKDNVTHSDLPHPDDLSKHEESQFQVNYE---PQSTPKEDGAPAQEKELPTVTSDDESKTPGASLESTLDRK------PEVKSTIEQHEAVENIPILPQGNTVVEENEMKSISLQQQTATDIPEAHGDRVEQPKSLLNEYNLGDKVEETISTLSEKHKDLVDAIEDSNDAYLSKDGKLVVDFLQAIHAAEKRQAELDAHIFAEEKRKMKEKYEKELKDARARELMYAEETAIVDKELNRERLKATAALKSLREELEDKLRIELEQKETEAESRLKNVQELSKAELAAAIASEKASLIEKMAEANLHINALCMAFYARSEEARQSHSVHKLALGALALEDALSQGLPIEKEIHALHTYLEGDAKDPLLDLVLSSIPKETQSKGTDTILQLQHKASFLVFDTLKGTLRHFSLIPPGGGGILTHSLAHVASSLKVKEADQSGDGIESLINRVESLLAEGKLSEAADSLENGVKGTQAAEVINDWLRQVRNRAITEQALTFVRAYATAISLT 651
| Match Name | Stats | Description |
|---|---|---|
| A0A5B7A9C7 | E-Value: 0.000e+0, PID: 54.62 | (Uncharacterized protein {ECO:0000313|EMBL:MPA5333... [more] |
| A0A5B7A9L1 | E-Value: 0.000e+0, PID: 54.31 | (Uncharacterized protein {ECO:0000313|EMBL:MPA5333... [more] |
| A0A5B7ABR8 | E-Value: 0.000e+0, PID: 54.10 | (Putative MICOS complex subunit MIC60 isoform X1 {... [more] |
| A0A6I9U964 | E-Value: 7.370e-170, PID: 47.34 | (MICOS complex subunit Mic60 {ECO:0000313|RefSeq:X... [more] |
| A0A2R6PAU2 | E-Value: 1.858e-169, PID: 46.79 | (MICOS complex subunit mic60 like {ECO:0000313|EMB... [more] |
| A0A6P6TKX8 | E-Value: 6.217e-167, PID: 46.70 | (MICOS complex subunit MIC60-like {ECO:0000313|Ref... [more] |
| A0A103XAZ9 | E-Value: 6.785e-166, PID: 49.58 | (Mitochondrial inner membrane protein Mitofilin {E... [more] |
| A0A6P6TBN4 | E-Value: 1.734e-165, PID: 46.44 | (MICOS complex subunit MIC60-like {ECO:0000313|Ref... [more] |
| A0A5B7AC34 | E-Value: 4.201e-164, PID: 62.61 | (Putative MICOS complex subunit MIC60 isoform X1 {... [more] |
| A0A834GAT6 | E-Value: 4.568e-163, PID: 46.36 | (Uncharacterized protein {ECO:0000313|EMBL:KAF7130... [more] |
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| Name | Description |
|---|---|
An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. We used BAC end sequences and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions. The resulting v2.0 assembly spans 421.5 Mb and contains 4,907 scaffolds (N50 of 12.7 Mb), accounting for ∼90% of the estimated genome size of 473 Mb. The scaftig N50 of 31.2 kb is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mb) of the assembled genome is included in only 60 superscaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4. There are a few different naming schemes for this assembly. First there is the Phytozome genome ID 388: The authors' sequences and gene predictions were also submitted to Phytozome, and can be accessed at this address: https://phytozome-next.jgi.doe.gov/info/Dcarota_v2_0 LNRQ01: These sequences were then assigned GenBank accession numbers starting at LNRQ01000001.1 which corresponds to DCARv2_Chr1, up to LNRQ01004826.1 which corresponds to an unincorporated contig, DCARv2_C10750146. These reside in bioproject PRJNA268187, which is a subproject of umbrella project PRJNA285926. Assembly GCA_001625215.1: The genome assembly was later defined an accession number GCA_001625215.1 for assembly ASM162521v1 which consists of only the 9 chromosome sequences and the plastid assembly, which have accession numbers from CM004278.1 to CM004286.1 for the chromosomes and CM004358.1 for the plastid. The mitochondrial genome was not included because it is classified as an incomplete sequence. RefSeq: The assembly was then later added to RefSeq, and there another new set of identifiers was defined from NC_030381.1 to NC_030389.1 for the chromosomes, and from NW_016089425.1 to NW_016094239.1 for unincorporated scaffolds and contigs. These reside in bioproject PRJNA326436. Note that NCBI substituted different assembled organellar genomes from different genotypes for the RefSeq records. The NCBI Sequence report lists the correspondences between the various naming methods Link to the LNRQ01000000.1 master record at NCBI Raw Reads: Link to SRA accessions used for the genome assembly This genome is available in the CarrotOmics Blast Search | |
This analysis is a blastp search of all of the DCAR V1.0 Gene Prediction polypeptide sequences against combined ExPASy SwissProt and TrEMBL databases from Nov. 17, 2021. Prior to performing the blast search, the database was filtered to remove organisms not in the Viridiplantae, and also filtered to remove these same DCAR gene predictions. | |
For gene model prediction, mobile element–related repeats were masked using RepeatMasker. De novo prediction using AUGUSTUS v2.5.5, GENSCAN v.1.1.0, and GlimmerHMM-3.0.1 was trained using model species A. thaliana and S. lycoperisum training sets. The protein sequences of S. lycoperisum, Solanum tuberosum, A. thaliana, Brassica rapa, and Oryza sativa were mapped to the carrot genome using TBLASTN (BLAST All 2.2.23) and analyzed with GeneWise version 2.2.0. Carrot ESTs were aligned to the genome using BLAT and analyzed with PASA to detect spliced gene models. RNA-seq reads from 20 DH1 libraries were aligned with TopHat 2.0.9. Transcripts were predicted by Cufflinks. All gene models produced by de novo prediction, protein homology searches, and prediction and transcript-based evidence were integrated using GLEAN v1.1. Putative gene functions were assigned using the best BLASTP match to SwissProt and TrEMBL databases. Gene motifs and domains were determined with InterProScan version 4.7 against the ProDom, PRINTS, Pfam, SMART, PANTHER, and PROSITE protein databases. GO IDs for each gene were obtained from the corresponding InterPro entries. All genes were aligned against KEGG (release 58) proteins. Data from this analysis can be viewed in JBrowse here. |