MMDFCKKSFYTLFNTASTAFTLPKEDSADNHHRNTPLPVTDCGAGLNILA
NSTAPPKFDNVIDSSSLINIPVKSDQTETGLKVLNSGDTDKLASCTESLG
FESCNERSLNNVLESSEKSRDDGKSRKFNKKNKELKRKSFPPPLSSFTDS
GKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQSDQKKE
GAITSTDAAGEKLSDGKVLKGWKFSTTNGGGGEDCRRVHEQRNMHGWAQQ
CVSIR*
| Relationships |
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| The polypeptide, DCAR_003308, derives from mRNA, DCAR_003308. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A5B6Z2A9 ((Putative SPX and EXS domain-containing protein 5-like {ECO:0000313|EMBL:MPA37958.1}))
HSP 1 Score: 149.058 bits (375), Expect = 4.291e-41
Identity = 107/288 (37.15%), Postives = 150/288 (52.08%), Query Frame = 0
Query: 1 MMDFCKKSFYTLFNTASTAFTLPKEDSADNHHRNTPLPVTDCGAGLNILANSTAPPKFDNVIDSSSLINIPVKSDQTETGLKVLN--SGDTDKLASCTESLGFESCNERSLNNVLESSEKSRD-DGKSRKFNKKNKELKR------------KSFPPPLSSFTDSGKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQSDQKKEGAITSTDAAGEKLS-----DGKVLKG------WKFSTTNGGGGEDCRRVHE-------QRNMHGWAQQCVSIR 255
MM FCKKS ++ N A+++ T+ E H + +P G GL+ + S + NV++S+++ + P G+ L+ G D L SCTESLGFES +ER +++ + + + F K L R K FPPPLSS GKP FFLR VRK+GRL+L EV+INRPE RASRE+GRLRLHL++ D + + E + D +VL G W+F T+ GGG+ RR HE N+HGW+Q CV+I+
Sbjct: 5 MMSFCKKSVHSFLNFANSSETVTVES---RRHCSNIIPSPAGGGGLSFITLSGDIQRPANVVESAAVKSAPSSPKIHHGGIGFLDYVGGSVDGLISCTESLGFESSDERRVDDDDHHHHQIENINNDELLFLKTTPPLIRSRWKRIMAKNEVKKFPPPLSSLNHDGKPNFFLRSVRKDGRLELMEVKINRPEIFRASREDGRLRLHLIRDDDEDADVEEQAETEEEDVEEKIEKDEEVLHGEHRANEWRFPATS-GGGDGFRRCHELVSHHHCHHNLHGWSQHCVTIK 288
Match: A0A068VAU5 ((Uncharacterized protein {ECO:0000313|EMBL:CDP17975.1}))
HSP 1 Score: 144.821 bits (364), Expect = 2.054e-39
Identity = 100/288 (34.72%), Postives = 143/288 (49.65%), Query Frame = 0
Query: 1 MMDFCKKSFYTLFNTAST----AFTLPKEDSADNHHRNTPLPVTDCGAGLNILANSTAPPKFDNVIDSSSLINIPVKSDQTETGLKVLNSGDT-DKLASCTESLGFESCNERSLNN------VLESSEKSRDDGKSRKFNKKNKELKRKSFPPPLSSFTDSGKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQSDQKKEGAITSTDAAGEKLSDGKVL----KGWKFSTTNGGGGEDCRRVHEQ------------------RNMHGWAQQCVSIR 255
M+ FCKKS + +++ LP +HHR T G T PP F N+ + + + K D G G T D L SCTESLGFES +ER +++ V+E R+ ++ +++ + + FPPPLSS GKPTFFLRPVRK+G+L+L EV+I R E LRASRE+GRLRLHL++++ + + E+L D ++ +GW+ GGGGE R HEQ +++ W Q CV+IR
Sbjct: 1 MITFCKKSVHNFLGSSNANDNGTVDLP---PFLHHHRQN---TTSDGQQPPDAIEKTPPPHFSNLFGTGTTLAARAKRDPGGMGFMDDVGGSTVDGLMSCTESLGFESSDERRVDDQIENLDVIEELCSRRESMAGSRWKREHAKREASQFPPPLSSLNQDGKPTFFLRPVRKDGKLELQEVKIGRQEILRASREDGRLRLHLIKNEDEDFEEDYEEEEEEEELEDRAMVEERAEGWQIPANPGGGGEGFLRCHEQVSHHQNHHHCCHGRHGHHHDLNVWRQHCVTIR 282
Match: A0A5B6Z1S3 ((Uncharacterized protein {ECO:0000313|EMBL:MPA37959.1}) (Fragment))
HSP 1 Score: 139.813 bits (351), Expect = 1.098e-37
Identity = 95/261 (36.40%), Postives = 133/261 (50.96%), Query Frame = 0
Query: 30 NHHRNTPLPVTDCGAGLNILANSTAPPKFDNVIDSSSLINIP-------VKSDQTETGLKVLNSGDTDKLASCTESLGFESCNERSLNNVLESSEKSRDDGKSRK--------FNKKNKELKRKSFPPPLSSFTDSGKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQSDQKKEGAITSTDAAGEKLSDGKVLKG-------------WKFSTTNGGGGEDCRRVHE-------QRNMHGWAQQCVSIR 255
+H + P P GL + S + NVI+S+++ + P K D G G D L SCTESLGFES +ER ++N + + DD K + KKN+++K+ FPPPLSS G+P FFLRPVRK+GRL+L EV+INRPE LRASR++GRLRLHL++ + + + + + + W F N GGG+ R HE N+HGW+Q+CV+IR
Sbjct: 18 HHCQKIPSPAA---GGLCFITFSGEIQRPANVIESAAVKSAPSSTTVSPAKIDPGGIGFLDEVGGSVDGLMSCTESLGFESSDERRVDNYQIVNMNNDDDQLCSKTTPLVRSRWKKKNEDVKK--FPPPLSSLNHDGRPNFFLRPVRKDGRLELTEVKINRPEILRASRQDGRLRLHLIREEDIDVEETEEEEEEEYQEEEVEEMIEDEDKEQEEERAGEWWFPAAN-GGGDGVRWCHELVRHHHHHHNLHGWSQRCVTIR 272
Match: A0A6A2XYD6 ((Uncharacterized protein {ECO:0000313|EMBL:KAE8675360.1}))
HSP 1 Score: 139.813 bits (351), Expect = 2.394e-37
Identity = 108/310 (34.84%), Postives = 148/310 (47.74%), Query Frame = 0
Query: 2 MDFCKKSFYTLFNTASTAFTLPKEDSADNHHRNTPLPVTDCGAGLNILANSTAPPKFDNVIDSSSL--INIPVKSDQTETGLKVLN-----SGDTDKLASCTESLGFESCNERSLNNVLESSEKSRDDGKSRKFNKKNKELKR------KSFPPPLSSFTDSGKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQSD---------------------QKKEGAITSTDAAGEKLSD-------------GKVLKGWKFSTTNGGGGEDCRR-VHEQRN--------MHGWAQQCVSIR 255
M +C +Y F F S N P + CG GL + +N P NV++SSSL +N S ++ V+ G+ D L SCTESLGFESC+E+ +N+ + E +++ + R NKK E KR K FPPPLSS +G+P F+L+PVR NGRL+L EV+I+RPE L A RENGRLRLHLV+SD ++++G + E++ K+ + W + NG G C VH R+ MH W Q CVSIR
Sbjct: 1 MPYCYLYYYAQFMLNKYYFGKKSVHSFLGL-SNKASPHSKCGLGL-VFSNEYNP----NVVESSSLPLLNTKPMSSLSKKDPGVIRFMDDMGGEVDGLTSCTESLGFESCSEKRVNDE-DEYEFCKEEIRGRWRNKKRVEEKRSDDKRDKKFPPPLSSLNQNGRPCFYLKPVRANGRLELTEVKIHRPEILLAVRENGRLRLHLVRSDICCKFNEDEEREHEEVHDLHEEEEKGDVCIKFNEDEEIEQEVHDLHEEEEEEGMKLQELWNY-RVNGEGSSRCHEMVHYHRHHGINGHHSMHVWRQPCVSIR 302
Match: A0A1U7YI06 ((SPX and EXS domain-containing protein 5-like {ECO:0000313|RefSeq:XP_009803742.1}))
HSP 1 Score: 138.658 bits (348), Expect = 1.274e-36
Identity = 105/306 (34.31%), Postives = 156/306 (50.98%), Query Frame = 0
Query: 1 MMDFCKKSFYTLFNTASTA-------FTLPKEDSADNHHRNTPLPVTDCGAGLNILANSTAPPKFDNVIDSSSLINIPVKSDQTETG-LKVLN--SGDTDKLASCTESLGFESCNERSLNNVLESSEKSRDDGKSRK--------------FNKKNKELKRKSFPPPLSSFTDSGKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQS---------------DQKKEGAITSTDAAGEKL-SDGKVLKG-WKFSTTNGGGGEDCRRVH----------EQRNMHGWAQQCVSIR 255
MM C K+ + + A++ F+LP+ RN T AG +I T P +N + S+++ P +++ + G + L+ G D L SCTESLGFES +ER++++ +E + +DD SRK + + N E K K FPPPLSS GKP FF+R VRK+GRL+L EV+I+RPE L ASR++GRLRLHL+++ D ++E T + E L +G+ G WKF T+GG G+ RR + + ++H W Q CV+ R
Sbjct: 45 MMSLCNKNVHPFLSLANSKHSGTLLDFSLPR--------RNI---FTAASAGGSI---DTQNP--NNYLVSTAMTPPPATAEKKDPGGIGFLDDVGGSVDGLMSCTESLGFESSDERTVDDQIE--DHDQDDLNSRKSYSTNMASYSNSKCWQRSNSEKKEKKFPPPLSSLNQDGKPNFFMRAVRKDGRLELTEVKISRPETLLASRQDGRLRLHLIRNEEEEETEEENDDFPLDDEEEVIETIQENNKEILDEEGEEKVGEWKFPVTSGGSGDGVRRCYGGHHHHGHNNHRHDLHVWRQHCVTTR 332
Match: A0A2R6R311 ((Protein FAF-like {ECO:0000313|EMBL:PSS19631.1}))
HSP 1 Score: 135.961 bits (341), Expect = 4.829e-36
Identity = 101/285 (35.44%), Postives = 146/285 (51.23%), Query Frame = 0
Query: 1 MMDFCKKSFYTLFNTASTAFTLPKEDSADNHH-RNTPLPVTDCGAGLNILANSTAPPKFDNVIDSSSLINIPVKSDQTET--------------GLKVLNS--GDTDKLASCTESLGFESCNERSLNNVLESSEKSRDDGKSRKFNKKNKELKRKSFPPPLSSFTDSGKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQ----SDQKKEGAITST----DAAGEKLSDGKVLKGWKFSTTNGGGGEDCRRVHEQRNMH-----GWAQQCVSIR 255
M++FC KS +L ++ E+ HH RN P P T GL +S K NV++S+++ P ++ G+ L+ G D L SCTESLGFES +ER + SR K R+ + K + K+FPPPLSS + +GK TFFL PVR++GRL+L EV+I+R E LRASRE+GRLRL L+ DQ++ T+ + ++ + ++ + W F+ N G E R+ HE N H W+Q CV+IR
Sbjct: 14 MLNFCMKSVRSLLGFVNST---NHENLITPHHSRNIPSPAT----GLASATSSDNTRKSANVVESAAIKPTPSTTEAAAAKHPPFAAARRKDPGGIGFLDEVGGSVDGLTSCTESLGFESSDER----LTGGETSSRTTSKKRRRVVEYKADEAKTFPPPLSSLSRNGKLTFFLLPVRRDGRLELTEVKIDRQEVLRASREDGRLRLSLITDVDVEDQEETEDTTTVMEEDEREEDREEEEEIGEKWVFTVAN-GDEEGFRQCHEMANHHHHILPAWSQHCVTIR 286
Match: A0A6P6WGC4 ((protein FANTASTIC FOUR 1 {ECO:0000313|RefSeq:XP_027114533.1}))
HSP 1 Score: 135.191 bits (339), Expect = 2.024e-35
Identity = 96/320 (30.00%), Postives = 149/320 (46.56%), Query Frame = 0
Query: 1 MMDFCKKSFYTLFNTAST----AFTLPKEDSADNHHRNTPLPVTDCGAGLNILANSTAPPKFDNVIDSSSLINIPVKSDQTETGLKVLNSGDTDKLASCTESLGFESCNERSLNN------VLESSEKSRDDGKSRKFNKKNKELKRKSFPPPLSSFTDSGKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQSDQKKEGAITSTDAAG-------------------------EKLSDGKV------------LKGWKFSTTNGGGGEDCRRVHEQ------------------RNMHGWAQQCVSIR 255
M+ FCKKS + +++T LP +HH+NT +D + + + P F N+ +S+ + K D G G D L SCTESLGFES +ER +++ V+E R+ ++ +++ + + + FPPPLSS GKPTFFLRPVRK+G+L+L EV+I R E LRASRE+GRLRLHL++++ + + +++ +G++ +GW+ GGGGE R HEQ +++ W Q C++IR
Sbjct: 1 MITFCKKSVHNFLGSSNTNDNGTVDLPS--FLHHHHQNT---TSDGQQPPDAIEKT---PHFSNLFGTSTTLATRTKRDPGGMGFV---GGSVDGLMSCTESLGFESSDERRVDDQIENLDVIEELCSRRESMAGSRWKREHVKREARQFPPPLSSLNQDGKPTFFLRPVRKDGKLELQEVKIGRQEILRASREDGRLRLHLIKNEDEDFEEEEEEEEEEEEEEEEVEERAVQEEENMQEFQENVQEMEEGQIGEEEVKEMVEERAEGWQIPANPGGGGEGFLRCHEQVSHHQNHHHHHHGRHGHHHDLNVWRQHCLTIR 309
Match: A0A1S4AI03 ((protein FANTASTIC FOUR 1-like {ECO:0000313|RefSeq:XP_016476317.1}))
HSP 1 Score: 130.568 bits (327), Expect = 1.320e-34
Identity = 83/210 (39.52%), Postives = 115/210 (54.76%), Query Frame = 0
Query: 87 GDTDKLASCTESLGFESCNERSLNNVLESSEKSRDDGKSRK--------------FNKKNKELKRKSFPPPLSSFTDSGKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQS---------------DQKKEGAITSTDAAGEKL-SDGKVLKG-WKFSTTNGGGGEDCRRVH----------EQRNMHGWAQQCVSIR 255
G D L SCTESLGFES +ER++++ +E ++ DD SRK + + N E K K FPPPLSS GKP FF+R VRK+GRL+L EV+I+RPE L ASR++GRLRLHL+++ D ++E T + E L +G+ G WKF T+GG + RR + + ++H W Q CV+ R
Sbjct: 24 GSVDGLMSCTESLGFESSDERTVDDQIEDHDQ--DDLNSRKSYSTNMASYSNSKCWQRSNSEKKEKKFPPPLSSLNQDGKPNFFMRAVRKDGRLELTEVKISRPETLLASRQDGRLRLHLIRNEEEEETEEENDNFPLDDEEEVIETIQENNKEILDEEGEEKVGEWKFPVTSGGSEDGVRRCYGGHHHHSHNNHRHDLHVWRQHCVTTR 231
Match: A0A1S3ZU08 ((protein FANTASTIC FOUR 4-like {ECO:0000313|RefSeq:XP_016467814.1}))
HSP 1 Score: 131.339 bits (329), Expect = 2.763e-34
Identity = 99/296 (33.45%), Postives = 139/296 (46.96%), Query Frame = 0
Query: 1 MMDFCKKSFYTLFNTASTA-------FTLPKEDSADNHHRNTPLPVTDCGAGLNILANSTAPPKFDNVIDSSSLINIPVKSDQTETGLKVLNSGDTDKLASCTESLGFESCNERSLNNVLESSEKSRDDGKSRK---------------FNKKNKELKRKSFPPPLSSFTDSGKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQSDQKKEGAITSTDAAGEKLSDGKV-----------LKGWKFSTTNGGGGEDCRRVH----------EQRNMHGWAQQCVS 253
MM FC K+ + N A+ F+LP+ + +T P + + S PP K D G G D L SCTESLGFES +ER++++ +E ++ DD RK N + KE+K+ FPPPLSS GKP FF+R VRK+GRL+L EV+I RPE L ASR++GRLRLHL++ D+++E T E L D + + WKF T+GG G+ RR + + ++H W Q CV+
Sbjct: 1 MMSFCNKNVHPFLNLANAKDNGTVLDFSLPRRNIFTGGSIDTQNPTN------YLESTSMTPP-----------TTAGEKKDPGGIGFLDDVGGSVDGLMSCTESLGFESSDERTVDDQIEDHDQ--DDFNPRKSYMASYSNSRCWQRSINSEKKEIKK--FPPPLSSLNQDGKPNFFMRAVRKDGRLELTEVKIGRPETLLASRQDGRLRLHLIR-DEEEEENEDFTLEREEHLDDEEEMIETVEEEEDKVAEWKFPVTSGGSGDGVRRCYGGHHHHRHNNHRHDLHVWRQHCVT 274
Match: W9SXK1 ((Uncharacterized protein {ECO:0000313|EMBL:EXC31833.1}))
HSP 1 Score: 131.339 bits (329), Expect = 3.529e-34
Identity = 104/301 (34.55%), Postives = 148/301 (49.17%), Query Frame = 0
Query: 1 MMDFCKKSFYTLFNTASTAFTLPKEDSADNHHRNTPLPVTDCGA-GLNILANSTAPPKFDNVIDSSSLIN--------IPVKSDQTETGLKVLNSGDTDKLASCTESLGFESCNERSLNN-----VLESSEKSRDDGKSRKFNKK----NKELKRKSFPPPLSSFTDSGKPTFFLRPVRKNGRLKLNEVQINRPECLRASRENGRLRLHLVQSDQKKEGAITST-----------DAAGEKLSDGKV-------------LKGWKFSTTNGGGGEDCRRVHEQRN----MHGWAQQCVSIR 255
MM FC+KS ++L + + D+AD+ N P C A GL + NV++SSS+I+ K D G G D L SCTESLGFES +ER +++ L S+++ K K+ K+ +KE+KR FPP LSS +G+P+FFLRPVRK+GRL+L EV+INRPE LRA R +GRLRLHL++ D+ ++ D EK+ + + + WK ++ G G RR H+ N +H W CV+ R
Sbjct: 1 MMSFCRKSVHSLLGLTAASV-----DAADHRPHNVLNPPWKCQALGLVTATSEIIRRPSPNVLESSSMISQNSPPPSPPTRKKDPRGIGFIDDIGGGVDGLMSCTESLGFESSDERRVDDDEEEFSLVSNDERPWTSKKVKWRKRMSGSSKEVKR--FPPLLSSLNRNGQPSFFLRPVRKDGRLELTEVRINRPEILRAYRGDGRLRLHLIRDDEDEDEDYIDEEEKQQEQGEDDDIREEKVEESVIREEDEEEEERNVNGEEWKIPVSSTGDG--FRRCHDVANHHHHLHVWRPHCVTTR 292
| Match Name | Stats | Description |
|---|---|---|
| A0A5B6Z2A9 | E-Value: 4.291e-41, PID: 37.15 | (Putative SPX and EXS domain-containing protein 5-... [more] |
| A0A068VAU5 | E-Value: 2.054e-39, PID: 34.72 | (Uncharacterized protein {ECO:0000313|EMBL:CDP1797... [more] |
| A0A5B6Z1S3 | E-Value: 1.098e-37, PID: 36.40 | (Uncharacterized protein {ECO:0000313|EMBL:MPA3795... [more] |
| A0A6A2XYD6 | E-Value: 2.394e-37, PID: 34.84 | (Uncharacterized protein {ECO:0000313|EMBL:KAE8675... [more] |
| A0A1U7YI06 | E-Value: 1.274e-36, PID: 34.31 | (SPX and EXS domain-containing protein 5-like {ECO... [more] |
| A0A2R6R311 | E-Value: 4.829e-36, PID: 35.44 | (Protein FAF-like {ECO:0000313|EMBL:PSS19631.1})[more] |
| A0A6P6WGC4 | E-Value: 2.024e-35, PID: 30.00 | (protein FANTASTIC FOUR 1 {ECO:0000313|RefSeq:XP_0... [more] |
| A0A1S4AI03 | E-Value: 1.320e-34, PID: 39.52 | (protein FANTASTIC FOUR 1-like {ECO:0000313|RefSeq... [more] |
| A0A1S3ZU08 | E-Value: 2.763e-34, PID: 33.45 | (protein FANTASTIC FOUR 4-like {ECO:0000313|RefSeq... [more] |
| W9SXK1 | E-Value: 3.529e-34, PID: 34.55 | (Uncharacterized protein {ECO:0000313|EMBL:EXC3183... [more] |
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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. |