MEAQTMKKPINIKMDSEKTADKEEQDGKNKTIVHSYGSHVDEEEERKIEC
MRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIP
KGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEE
LKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQ
DYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETL
MEDIDESQLPAIYGGKLPLVPIQHA*
| Relationships |
|---|
| The polypeptide, DCAR_025641, derives from mRNA, DCAR_025641. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A5B7B8X5 (CRAL-TRIO domain-containing protein {ECO:0000259|PROSITE:PS50191})
HSP 1 Score: 368.622 bits (945), Expect = 6.361e-127
Identity = 175/261 (67.05%), Postives = 208/261 (79.69%), Query Frame = 0
Query: 13 KMDSEKTADKEEQDGKNKTIVHSYGSHVDEEEERKIECMRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIPKGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEELKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQDYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETLMEDIDESQLPAIYGGKLPLVPIQ 273
KM+SE+ EE+ K+ + +E E+ K+ MR VE+ DPS KEVD+ +RRFLRARD DIEKASAMF+KYLKW+QTF+P GS+S S+I+N LAQNK F+QG+DK+GRPITV F GRH K GGVEE KRF+VFAL ++CSRM GQEKFVVI DL+GWGY NSD+R + AL++LQDYYPERLGKL IVHVP IFMTVWK++YPFIDN TKKK+VFVENKRLK TL+EDIDESQLP IYGGK+PLVPIQ
Sbjct: 26 KMESEEHTTNEERTEKSVEC----SNESNEVEQNKVRLMRAFVERQDPSSKEVDDLMIRRFLRARDLDIEKASAMFLKYLKWRQTFVPNGSISASQITNDLAQNKMFMQGLDKKGRPITVAFAGRHFHHK---GGVEEFKRFVVFALDRLCSRMPTGQEKFVVIGDLEGWGYSNSDIRAYLGALSILQDYYPERLGKLFIVHVPYIFMTVWKVVYPFIDNTTKKKIVFVENKRLKSTLLEDIDESQLPEIYGGKMPLVPIQ 279
Match: A0A067F360 (CRAL-TRIO domain-containing protein {ECO:0000259|PROSITE:PS50191})
HSP 1 Score: 361.303 bits (926), Expect = 1.130e-124
Identity = 165/238 (69.33%), Postives = 198/238 (83.19%), Query Frame = 0
Query: 38 SHVDEEEERKIECMRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIPKGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEELKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQDYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETLMEDIDESQLPAIYGGKLPLVPIQHA 275
S++DE+EE KI MR LVEK DPS KEVD+PTLRRFLRARD D+EKAS MF+KYLKW+QTF+P GS+S SE+ N L+QNK F+QG DK+GRPI + G RH K+ GG+EE KRF+V+ L KICSRM GQEKFVVI DL+GWGY NSD+R + AL++LQDYYPERLGKL IVH P IFMTVWK++YPFIDNNTKKK+VFV++K+LK TL+E+IDESQ+P IYGG+LPLVPIQ
Sbjct: 8 SNIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKYLKWRQTFVPNGSISLSEVPNELSQNKMFMQGFDKKGRPIATVLGARHFQNKL--GGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVYPFIDNNTKKKIVFVQDKKLKSTLLEEIDESQIPEIYGGQLPLVPIQET 243
Match: V4TAF0 (CRAL-TRIO domain-containing protein {ECO:0000259|PROSITE:PS50191})
HSP 1 Score: 359.762 bits (922), Expect = 5.507e-124
Identity = 164/238 (68.91%), Postives = 198/238 (83.19%), Query Frame = 0
Query: 38 SHVDEEEERKIECMRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIPKGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEELKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQDYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETLMEDIDESQLPAIYGGKLPLVPIQHA 275
S++DE+EE KI MR LVEK DPS KEVD+PTLRRFLRARD D+EKAS MF+KYLKW+QTF+P GS+S SE+ N L+QNK F+QG DK+GRPI + G RH K+ GG+EE KRF+V+ L KICSR+ GQEKFVVI DL+GWGY NSD+R + AL++LQDYYPERLGKL IVH P IFMTVWK++YPFIDNNTKKK+VFV++K+LK TL+E+IDESQ+P IYGG+LPLVPIQ
Sbjct: 11 SNIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKYLKWRQTFVPNGSISLSEVPNELSQNKMFMQGFDKKGRPIATVLGARHFQNKL--GGLEEFKRFVVYILDKICSRIPPGQEKFVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVYPFIDNNTKKKIVFVQDKKLKSTLLEEIDESQIPEIYGGQLPLVPIQET 246
Match: A0A5J5BG32 (CRAL-TRIO domain-containing protein {ECO:0000259|PROSITE:PS50191})
HSP 1 Score: 358.607 bits (919), Expect = 3.174e-123
Identity = 169/261 (64.75%), Postives = 210/261 (80.46%), Query Frame = 0
Query: 13 KMDSEKTADKEEQDGKNKTIVHSYGSHVDEEEERKIECMRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIPKGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEELKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQDYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETLMEDIDESQLPAIYGGKLPLVPIQ 273
KM+SE+ + + + K + HS S +E E+ K+ MR VEK DPS KE D+ +RRFLRARD D+EKASAMF+KY+KWK+TF+P GS+S SE+ N +AQNK F+QG+DK+GRPITV+F GRH P+K GG++E KRF+VFAL K+CS M GQEKFVVI DL+GWGY NSD+R + AL++LQDYYPERLGKL IVHVP IFMTVWK++YPFIDNNTKKK+VFVENK+LK TL+EDIDESQ+P +YGGK+ LVPIQ
Sbjct: 12 KMESEEHTIEAKTE---KGVEHSNAS--NEMEQNKVRLMRAFVEKQDPSSKEEDDLMIRRFLRARDLDVEKASAMFLKYIKWKRTFVPNGSISVSEVPNEIAQNKMFMQGLDKKGRPITVVFAGRHFPQK---GGLDEFKRFVVFALDKLCSSMPTGQEKFVVIGDLKGWGYSNSDIRAYLGALSILQDYYPERLGKLFIVHVPYIFMTVWKIVYPFIDNNTKKKIVFVENKQLKSTLLEDIDESQVPDVYGGKMALVPIQ 264
Match: A0A7J7CBA3 (CRAL-TRIO domain-containing protein {ECO:0000259|PROSITE:PS50191})
HSP 1 Score: 351.288 bits (900), Expect = 1.894e-120
Identity = 164/260 (63.08%), Postives = 204/260 (78.46%), Query Frame = 0
Query: 14 MDSEKTADKEEQDGKNKTIVHSYGSHVDEEEERKIECMRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIPKGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEELKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQDYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETLMEDIDESQLPAIYGGKLPLVPIQ 273
MDS++T KEE + + S+ +E E+ K+ MR E+ DPS KEVD+ T+RRFLRARD ++EKASAMF+KYLKW+QTF+P ++S +E+ N +AQNK F+QG+DKQGRPI ++FG RH KI GG +E KRF+V+ L K+CSR+ GQEKFVVI DL+GWGY NSD+RG +AALT LQDYYPERLGKL VHVP IFMT WK+IYPFID+NTKKK++FVENKRL TL+EDID+SQLP IYGGKLP+VPI
Sbjct: 1 MDSQETKVKEEAGHQEDDM----KSNFNETEKTKLCLMRAFAERQDPSSKEVDDLTIRRFLRARDLNVEKASAMFLKYLKWRQTFVPNNTISITEVPNEIAQNKMFMQGLDKQGRPIAIVFGARHFQNKI--GGADEFKRFVVYGLDKLCSRIPPGQEKFVVIGDLKGWGYSNSDIRGYLAALTTLQDYYPERLGKLFFVHVPSIFMTAWKIIYPFIDSNTKKKIIFVENKRLTSTLLEDIDQSQLPEIYGGKLPVVPIH 254
Match: A0A6N2C4T7 (CRAL-TRIO domain-containing protein {ECO:0000259|PROSITE:PS50191})
HSP 1 Score: 349.362 bits (895), Expect = 1.630e-119
Identity = 165/254 (64.96%), Postives = 202/254 (79.53%), Query Frame = 0
Query: 22 KEEQDGKNKTIVHSYGSHVDEEEERKIECMRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIPKGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEELKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQDYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETLMEDIDESQLPAIYGGKLPLVPIQHA 275
K +Q G+ VH + ++E+E KI +R +VEK DPS KEVD+ +RRFLRARD D++KASAM +KYLKWK++F+P G +S +EI N +A NK FLQGVDK GRPI V+FGGRH+P K GG+EE KRF+V AL K+CSR + G+EKFVVI DLQG+GY NSDVR + AL++LQD YPERLGKL++VHVP IF T+WKL+YPFIDNNTKKK+ FVENKRL ETL+EDIDESQLP IYGGK+PLVPI A
Sbjct: 20 KLQQQGQEIQSVHCDDATINEQEMNKISAVRAVVEKQDPSSKEVDDFAIRRFLRARDLDVDKASAMLLKYLKWKKSFVPNGYISPTEIPNEIAHNKMFLQGVDKLGRPIAVVFGGRHMPNK--QGGLEEFKRFVVLALDKLCSRTSPGREKFVVIGDLQGFGYSNSDVRAYLGALSILQDCYPERLGKLIVVHVPYIFWTMWKLVYPFIDNNTKKKITFVENKRLTETLLEDIDESQLPDIYGGKMPLVPIHEA 271
Match: M1B458 ((Polyphosphoinositide binding protein {ECO:0000313|EnsemblPlants:PGSC0003DMT400036745}))
HSP 1 Score: 349.362 bits (895), Expect = 1.921e-119
Identity = 165/254 (64.96%), Postives = 201/254 (79.13%), Query Frame = 0
Query: 22 KEEQDGKNKTIVHSYGSHVDEEEERKIECMRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIPKGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEELKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQDYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETLMEDIDESQLPAIYGGKLPLVPIQHA 275
K +Q GK +H + ++EEE KI +R +VEK DPS KEVD+ +RRFLRARD D+EKAS M +KYLKWK++F+P G +S +EI N +A NK FLQGVDK GRPI V+FGGRH+P K GG+EE KRF+V AL K+CSR + G+EKFVVI DLQG+GY NSDVR + AL++LQD YPERLGKL++VHVP IF T+WKL+YPFIDNNTKKK+ FVENKRL ETL++DIDESQLP IYGGK+PLVPI A
Sbjct: 20 KLQQQGKEIQSIHCDDATINEEEMNKISLVRAVVEKQDPSSKEVDDFAIRRFLRARDLDVEKASTMLLKYLKWKKSFVPNGYISPTEIPNEIAHNKMFLQGVDKLGRPIAVVFGGRHMPNK--QGGLEEFKRFVVLALDKLCSRTSPGREKFVVIGDLQGFGYSNSDVRAYLGALSILQDCYPERLGKLIVVHVPYIFWTMWKLVYPFIDNNTKKKITFVENKRLTETLLQDIDESQLPDIYGGKMPLVPIHEA 271
Match: A0A1S4BFU9 ((random slug protein 5-like isoform X1 {ECO:0000313|RefSeq:XP_016487750.1}))
HSP 1 Score: 348.591 bits (893), Expect = 4.245e-119
Identity = 161/236 (68.22%), Postives = 199/236 (84.32%), Query Frame = 0
Query: 40 VDEEEERKIECMRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIPKGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEELKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQDYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETLMEDIDESQLPAIYGGKLPLVPIQHA 275
+ E+E KIE MR +VEK DPS KEVD LRRFLRARD D+EKASAMF+KYLKW+Q+F+PKGS+S EI N +AQNK F+QGVDKQGRPI V+FGGRH+ KI GGVEE KRF+VFAL K+C+R + G+EKFV+I DLQG+GY NSDVR +AAL+++QD YPERLGK+L+V+ P +F T+WK++YPFIDNNTKKK++FVE+KRL+ TL++DIDESQLP YGGK+PLVPIQ A
Sbjct: 41 ITEQENYKIELMRAVVEKKDPSSKEVDEYALRRFLRARDLDVEKASAMFLKYLKWRQSFVPKGSISVCEIPNEIAQNKMFMQGVDKQGRPIAVVFGGRHIQNKI--GGVEEFKRFIVFALDKLCARTSPGREKFVIIGDLQGFGYSNSDVRAYLAALSIVQDCYPERLGKVLLVNAPYLFCTLWKMLYPFIDNNTKKKIMFVESKRLRATLLQDIDESQLPEAYGGKMPLVPIQDA 274
Match: A0A3Q7FVE9 (CRAL-TRIO domain-containing protein {ECO:0000259|PROSITE:PS50191})
HSP 1 Score: 347.436 bits (890), Expect = 8.787e-119
Identity = 164/254 (64.57%), Postives = 201/254 (79.13%), Query Frame = 0
Query: 22 KEEQDGKNKTIVHSYGSHVDEEEERKIECMRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIPKGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEELKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQDYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETLMEDIDESQLPAIYGGKLPLVPIQHA 275
K +Q G+ VH + ++E+E KI +R +VEK DPS KE D+ +RRFLRARD D++KASAM +KYLKWK++F+P G +S +EI N +A NK FLQGVDK GRPI V+FGGRH+P K GG+EE KRF+V AL K+CSR + G+EKFVVI DLQG+GY NSDVR + AL++LQD YPERLGKL++VHVP IF T+WKL+YPFIDNNTKKK+ FVENKRL ETL+EDIDESQLP IYGGK+PLVPI A
Sbjct: 20 KLQQQGQEIQSVHCDDATINEQEMNKISAVRAVVEKQDPSSKEFDDFAIRRFLRARDLDVDKASAMLLKYLKWKKSFVPNGYISPTEIPNEIAHNKMFLQGVDKLGRPIAVVFGGRHMPNK--QGGLEEFKRFVVLALDKLCSRTSPGREKFVVIGDLQGFGYSNSDVRAYLGALSILQDCYPERLGKLIVVHVPYIFWTMWKLVYPFIDNNTKKKITFVENKRLTETLLEDIDESQLPDIYGGKMPLVPIHEA 271
Match: A0A3Q7GX51 (CRAL-TRIO domain-containing protein {ECO:0000259|PROSITE:PS50191})
HSP 1 Score: 347.821 bits (891), Expect = 2.289e-118
Identity = 166/275 (60.36%), Postives = 212/275 (77.09%), Query Frame = 0
Query: 1 MEAQTMKKPINIKMDSEKTADKEEQDGKNKTIVHSYGSHVDEEEERKIECMRKLVEKHDPSVKEVDNPTLRRFLRARDQDIEKASAMFVKYLKWKQTFIPKGSVSESEISNHLAQNKQFLQGVDKQGRPITVLFGGRHLPKKIPDGGVEELKRFMVFALGKICSRMAAGQEKFVVIADLQGWGYCNSDVRGCIAALTLLQDYYPERLGKLLIVHVPCIFMTVWKLIYPFIDNNTKKKLVFVENKRLKETLMEDIDESQLPAIYGGKLPLVPIQHA 275
M + KP N K+ S++ +E + + I + ++E KIE MR LVEK DPS KE+D+ LRRFLRARD DIEK++AMF+KYLKW+Q+F+PKGS+ SEI N +AQNK F+QGVDKQG PI V+FGGRH+ K+ GGVEE KRF+VFAL K+C+R + G+EKF +I DLQ +GYCNSDVR +AAL+++QD YPERLGK+L+VHVP IF T+WK++YPFIDN+TKKK++FVENKRL TL++DIDESQLP YGGK+ LVPIQ A
Sbjct: 37 MRCDDVMKPNNDKLLSKQRMKQEAVATEKEGIQMQCDDTITDQEMNKIELMRALVEKQDPSSKEIDDYALRRFLRARDLDIEKSAAMFLKYLKWRQSFVPKGSILVSEIPNEIAQNKMFMQGVDKQGCPIAVVFGGRHIQNKL--GGVEEFKRFIVFALDKLCARTSPGREKFTIIGDLQNFGYCNSDVRAYLAALSIVQDCYPERLGKVLLVHVPYIFCTLWKILYPFIDNHTKKKIMFVENKRLTATLLQDIDESQLPETYGGKMQLVPIQDA 309
| Match Name | Stats | Description |
|---|---|---|
| A0A5B7B8X5 | E-Value: 6.361e-127, PID: 67.05 | CRAL-TRIO domain-containing protein {ECO:0000259|P... [more] |
| A0A067F360 | E-Value: 1.130e-124, PID: 69.33 | CRAL-TRIO domain-containing protein {ECO:0000259|P... [more] |
| V4TAF0 | E-Value: 5.507e-124, PID: 68.91 | CRAL-TRIO domain-containing protein {ECO:0000259|P... [more] |
| A0A5J5BG32 | E-Value: 3.174e-123, PID: 64.75 | CRAL-TRIO domain-containing protein {ECO:0000259|P... [more] |
| A0A7J7CBA3 | E-Value: 1.894e-120, PID: 63.08 | CRAL-TRIO domain-containing protein {ECO:0000259|P... [more] |
| A0A6N2C4T7 | E-Value: 1.630e-119, PID: 64.96 | CRAL-TRIO domain-containing protein {ECO:0000259|P... [more] |
| M1B458 | E-Value: 1.921e-119, PID: 64.96 | (Polyphosphoinositide binding protein {ECO:0000313... [more] |
| A0A1S4BFU9 | E-Value: 4.245e-119, PID: 68.22 | (random slug protein 5-like isoform X1 {ECO:000031... [more] |
| A0A3Q7FVE9 | E-Value: 8.787e-119, PID: 64.57 | CRAL-TRIO domain-containing protein {ECO:0000259|P... [more] |
| A0A3Q7GX51 | E-Value: 2.289e-118, PID: 60.36 | CRAL-TRIO domain-containing protein {ECO:0000259|P... [more] |
Pages
back to top| 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. |