MASTLNSNPVTTSPRESSRKKKKKRGQLKASSQSPENNQISWKSETQQQL
YSSKLVQALRQVRLDSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAI
LTNRLKLKFLKKAKRHRVPIADRRSAKKPKVSILKLKSKNLPAVQRKAKA
LGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALADLLSGGGSSSGA
SSSTQPQLDQNMDESSS*
| Relationships |
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| The polypeptide, DCAR_026988, derives from mRNA, DCAR_026988. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A4S4DMA6 (BHLH domain-containing protein {ECO:0000259|PROSITE:PS50888})
HSP 1 Score: 250.751 bits (639), Expect = 1.926e-82
Identity = 138/212 (65.09%), Postives = 164/212 (77.36%), Query Frame = 0
Query: 1 MASTLNSNPVTTSPRESSRKKKKKRGQLKAS---SQSPENNQISWKSETQQQLYSSKLVQALRQVRLDSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAILTNRLKLKFLKKAKRHRVPIADRRSAKKPKVSILKLKSKNLPAVQRKAKALGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALADLLSGGGSSSGAS---SSTQP 206
MASTL SNPVT S R K++K+ +++A+ +Q+P N WKSE QQQ+YSSKL+ ALRQVRL SSS + P R RAVR+ A RVLA TAKGKTRWSRAILTNRLKLKF+K KR RV + +KKP+VSIL+LKSKNLPA+QRK + LGRLVPGCRKEP PV+LEE DYI ALEMQI+AM+ALA+LLSG GSS+G SST+P
Sbjct: 2 MASTLISNPVTNSDRARESSKRRKKKKVQATRDQAQNP-NTSTPWKSEAQQQVYSSKLLHALRQVRLRSSSPAAPRRGRAVREAADRVLAVTAKGKTRWSRAILTNRLKLKFMKN-KRQRVKVTGSNRSKKPRVSILRLKSKNLPAMQRKVRVLGRLVPGCRKEPLPVILEEATDYIAALEMQIKAMSALAELLSGAGSSAGPQSQLSSTRP 211
Match: A0A7J7HE48 (BHLH domain-containing protein {ECO:0000259|PROSITE:PS50888})
HSP 1 Score: 247.284 bits (630), Expect = 4.844e-81
Identity = 136/212 (64.15%), Postives = 164/212 (77.36%), Query Frame = 0
Query: 1 MASTLNSNPVTTSPRESSRKKKKKRGQLKAS---SQSPENNQISWKSETQQQLYSSKLVQALRQVRLDSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAILTNRLKLKFLKKAKRHRVPIADRRSAKKPKVSILKLKSKNLPAVQRKAKALGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALADLLSGGGSSSGAS---SSTQP 206
MASTL SNPVT S R K++K+ +++A+ +Q+P N+ WKSE QQQ+YSSKL+ ALRQVRL SSS + P R RAVR+ A RVLA TAKGKTRWSRAILTNRLKLKF+K KR RV + +KKP+VSIL+LKSKNLPA+QRK + LGRLVPGCRKEP PV+LEE DYI ALEMQ++AM+ALA+LLSG SS+G SST+P
Sbjct: 2 MASTLISNPVTNSDRARESSKRRKKKKVQATRDQAQNP-NSSTPWKSEAQQQVYSSKLLHALRQVRLRSSSPAAPRRGRAVREAADRVLAVTAKGKTRWSRAILTNRLKLKFMKN-KRQRVKVTGSNRSKKPRVSILRLKSKNLPAMQRKVRVLGRLVPGCRKEPLPVILEEATDYIAALEMQVKAMSALAELLSGASSSAGPQSQLSSTRP 211
Match: A0A2R6PJJ1 ((Transcription factor bHLH147 like {ECO:0000313|EMBL:PSR92494.1}))
HSP 1 Score: 232.261 bits (591), Expect = 4.928e-75
Identity = 136/216 (62.96%), Postives = 159/216 (73.61%), Query Frame = 0
Query: 1 MASTLNSNPVTTSPRESSRKKKKKRGQLKAS---SQSPE--NNQISWKSETQQQLYSSKLVQALRQVRLDSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAILTNRLKLKFLKKAKRHRVPIADRRSAKKPKVSILKLKSKNLPAVQRKAKALGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALADLLSGGGSSSGASSSTQPQLDQN 211
MASTL SNPVT S R K++K+ +L A+ SQ+P + WKS+ QQQ+YSSKL+QALRQ+R+ SSS + P RSRAVR+ A RVLA TAKGKTRWSRAILTNRLKLKF+K +R A KKP+VSI +LKSKNLPAVQRKA+ LGRLVPGCRKEP PV+LEE DYI ALEMQ+RAM+ALA+LLSG SG S ST L N
Sbjct: 1 MASTLVSNPVTNSDRARESSKRRKKKKLLATRDESQNPNAAHGSTQWKSDPQQQVYSSKLLQALRQLRI-SSSPTAPRRSRAVREVADRVLAVTAKGKTRWSRAILTNRLKLKFMKNKRRSPAASAAGDRLKKPRVSISRLKSKNLPAVQRKARVLGRLVPGCRKEPLPVILEEATDYIAALEMQVRAMSALAELLSG----SGPSGSTVTPLGSN 211
Match: A0A7J0GSY6 ((Basic helix-loop-helix (BHLH) DNA-binding superfamily protein {ECO:0000313|EMBL:GFZ13892.1}))
HSP 1 Score: 231.106 bits (588), Expect = 1.453e-74
Identity = 131/202 (64.85%), Postives = 154/202 (76.24%), Query Frame = 0
Query: 1 MASTLNSNPVTTSPRESSRKKKKKRGQLKAS---SQSPE--NNQISWKSETQQQLYSSKLVQALRQVRLDSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAILTNRLKLKFLKKAKRHRVPIADRRSAKKPKVSILKLKSKNLPAVQRKAKALGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALADLLSGGGSS 197
MASTL SNPVT S R K++K+ +L A+ SQ+P + WKS+ QQQ+YSSKL+QALRQ+R+ SSS + RSRAVR+ A RVLA TAKGKTRWSRAILTNRLKLKF+K +R A KKP+VSIL+LKSKNLPAVQRKA+ LGRLVPGCRKEP PV+LEE DYI ALEMQ+RAM+ALA+LLSG G S
Sbjct: 1 MASTLVSNPVTNSDRARESSKRRKKKKLLATRDESQNPNAAHGSTQWKSDPQQQVYSSKLLQALRQLRI-SSSPTAQRRSRAVREVADRVLAVTAKGKTRWSRAILTNRLKLKFMKNKRRSPAASAAGDRLKKPRVSILRLKSKNLPAVQRKARVLGRLVPGCRKEPLPVILEEATDYIAALEMQVRAMSALAELLSGSGPS 201
Match: A0A5J5AJH6 ((Uncharacterized protein {ECO:0000313|EMBL:KAA8531205.1}))
HSP 1 Score: 231.106 bits (588), Expect = 1.517e-74
Identity = 131/196 (66.84%), Postives = 155/196 (79.08%), Query Frame = 0
Query: 1 MASTLNSNPVTTS--PRESSRKKKKKRG-QLKASSQSPENNQIS--WKSETQQQLYSSKLVQALRQVRLDSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAILTNRLKLKFLKKAKRHRVPIADRRSAKKPKVSILKLKSKNLPAVQRKAKALGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALADLL 191
MAST+ SNP+T S RES++KKKKK+ ++ Q+P NNQ S WK E QQ++YSSKL+QALRQVRL SSS S P R RAVR+ A RVLA TAKG++RWSRAILTNRLKLKF+K KR RV + +KKP+VSIL+LKSKNLPAVQRKA LGRLVPGCRK+P PV+LEE DYI ALEMQ++AM ALA+LL
Sbjct: 1 MASTMISNPITNSDRARESAKKKKKKKSLAIRDQIQNPNNNQSSTQWKCEAQQKVYSSKLLQALRQVRL-SSSPSAPRRGRAVREAADRVLAVTAKGRSRWSRAILTNRLKLKFMKN-KRQRVTVTGNTRSKKPRVSILRLKSKNLPAVQRKASVLGRLVPGCRKQPLPVILEEATDYIAALEMQVKAMTALAELL 194
Match: A0A5J5A8F1 ((Uncharacterized protein {ECO:0000313|EMBL:KAA8527355.1}))
HSP 1 Score: 230.72 bits (587), Expect = 1.749e-74
Identity = 131/196 (66.84%), Postives = 154/196 (78.57%), Query Frame = 0
Query: 1 MASTLNSNPVTTS--PRESSRKKKKKRGQ-LKASSQSPENNQIS--WKSETQQQLYSSKLVQALRQVRLDSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAILTNRLKLKFLKKAKRHRVPIADRRSAKKPKVSILKLKSKNLPAVQRKAKALGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALADLL 191
MASTL SNPVT S R+S++KKKKK+ Q ++ +Q+P N S WKSE QQQ+YSSKL+QALR VRL SSS S P R R+VR+ A RVLA TAKG+TRWSRAILTNRLKLKF+K KR RV + +KKP++SIL+LKSKNLPAVQRK + LGRLVPGCRKEP PV+LEE DYI ALEMQ+RAM AL +LL
Sbjct: 1 MASTLISNPVTNSDRARDSAKKKKKKKSQAIRDETQNPNTNHDSTQWKSEVQQQVYSSKLLQALRGVRL-SSSPSAPRRGRSVREAADRVLAVTAKGRTRWSRAILTNRLKLKFMKN-KRQRVTVTGSTRSKKPRLSILRLKSKNLPAVQRKVRVLGRLVPGCRKEPLPVILEEATDYIAALEMQVRAMTALTELL 194
Match: A0A834HDQ1 ((Uncharacterized protein {ECO:0000313|EMBL:KAF7151218.1}))
HSP 1 Score: 229.565 bits (584), Expect = 3.881e-74
Identity = 120/192 (62.50%), Postives = 143/192 (74.48%), Query Frame = 0
Query: 1 MASTLNSNPVTTSPRESSRKKKKK-RGQLKASSQSPENNQISWKSETQQQLYSSKLVQALRQVRLDSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAILTNRLKLKFLKKAKRHRVPIADRRSAKKPKVSILKLKSKNLPAVQRKAKALGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALADLL 191
MAST+ SNP+T S R +SRKKKK + + SQ+P WKSE+QQQ YSSKL+ ALRQVR P R RAVR+ A RVLA TAKG+TRWSRAILTNRLKLKF+K +R RV +KKP+VS+L+L+ KNLPAV RKA+ LGRLVPGC+KEP PV+LEE DYI ALEMQ+RAM+ALA+LL
Sbjct: 1 MASTMISNPITNSNRATSRKKKKALQSASRDQSQNPNGATTQWKSESQQQAYSSKLLHALRQVR----PIPAPRRGRAVREAADRVLAVTAKGRTRWSRAILTNRLKLKFMKNNRRQRVVATAVSRSKKPRVSVLRLRCKNLPAVHRKARVLGRLVPGCKKEPLPVILEEATDYIAALEMQVRAMSALAELL 188
Match: A0A7J0GKY0 ((Sequence-specific DNA binding transcription factor {ECO:0000313|EMBL:GFZ11479.1}))
HSP 1 Score: 228.409 bits (581), Expect = 1.393e-73
Identity = 127/194 (65.46%), Postives = 150/194 (77.32%), Query Frame = 0
Query: 1 MASTLNSNPVTTSPRESSRKKKKKRGQLKAS---SQSP--ENNQISWKSETQQQLYSSKLVQALRQVRLDSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAILTNRLKLKFLKKAKRHRVPIADRRSAKKPKVSILKLKSKNLPAVQRKAKALGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALAD 189
MASTL SNPVT S R K++K+ +L A+ SQ+P ++ WKS+ QQQ+YSSKL+QALRQVR+ SSS + P RSRAVR+ A RVLA TAKGKTRWSRAILTNRLKLKF+K +R A KKP+VSIL+LKSKNLPAVQRKA+ LGRLVPGCRKEP PV+LEE DYI ALEMQ+RAM+ALA+
Sbjct: 1 MASTLVSNPVTNSDRARESSKRRKKKKLVATRDESQNPNADHGSTQWKSDAQQQVYSSKLLQALRQVRIGSSS-TAPRRSRAVREAADRVLAVTAKGKTRWSRAILTNRLKLKFMKNKRRSPAASAAGGRPKKPRVSILRLKSKNLPAVQRKARVLGRLVPGCRKEPLPVILEEATDYIAALEMQVRAMSALAE 193
Match: A0A5N6RC87 ((Uncharacterized protein {ECO:0000313|EMBL:KAE8076655.1}))
HSP 1 Score: 228.024 bits (580), Expect = 1.488e-73
Identity = 129/199 (64.82%), Postives = 148/199 (74.37%), Query Frame = 0
Query: 1 MASTLNSNPVTTSPRESSRKKKKKRGQLKASSQSPENNQISWKSETQQQLYSSKLVQALRQVRL----DSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAILTNRLKLKFLKKAKRHRVPIA----DRRSAKKPKVSILKLKSKNLPAVQRKAKALGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALADLL 191
MASTL SNPVT S R +KKKK ++ + ++N I WKSETQQQ+YSSKLVQAL QVRL S SA VP R RAVR+ A RVLA AKGKTRWSRAILT+RLKLKF KK KR RV A R S+KKPKVS+L+LK K LPAVQRK + LGRLVPGCRK+P PV+L+E DYI ALEMQ+RAM+ALA+ L
Sbjct: 1 MASTLISNPVTNSDRSKKKKKKK----IQEKDHNDDHNHIKWKSETQQQIYSSKLVQALSQVRLGPSPSSPSAEVPRRGRAVREAADRVLAVAAKGKTRWSRAILTSRLKLKFQKKHKRQRVVSAATGTSRSSSKKPKVSVLRLKGKCLPAVQRKVRVLGRLVPGCRKQPLPVILDEATDYIAALEMQVRAMSALAERL 195
Match: A0A5B6YXD1 ((Uncharacterized protein {ECO:0000313|EMBL:MPA36421.1}) (Fragment))
HSP 1 Score: 231.106 bits (588), Expect = 1.762e-73
Identity = 131/200 (65.50%), Postives = 155/200 (77.50%), Query Frame = 0
Query: 1 MASTLNSNPVTTS--PRESSRKKKKKRGQL---KASSQSPENNQISWKSETQQQLYSSKLVQALRQVRLDSSSASVPSRSRAVRDTAYRVLATTAKGKTRWSRAILTNRLKLKFLKKAKRHRVPIADRRSAKKPKVSILKLKSKNLPAVQRKAKALGRLVPGCRKEPFPVVLEETADYIVALEMQIRAMAALADLLSGGG 195
MASTL SNPVT S RES++KKKKK+ Q + + + +N WKSE QQQ+YSSKL+QALR+VR SSS S P R R+VR+ A RVLA TAKG+TRWSRAILT+RLKLKF+K KR RV + +KKP+VSIL+LKSKNLPAVQRK + LGRLVPGCRKEP PV+LEE DYI ALEMQ++AM ALA+LLSG G
Sbjct: 85 MASTLISNPVTNSDRARESAKKKKKKKSQAIRDETLNANTNHNSTQWKSEVQQQVYSSKLLQALRRVR-QSSSPSAPRRGRSVREAADRVLAVTAKGRTRWSRAILTSRLKLKFMKN-KRQRVTVTGNSRSKKPRVSILRLKSKNLPAVQRKVRVLGRLVPGCRKEPLPVILEEATDYIAALEMQVKAMTALAELLSGFG 282
| Match Name | Stats | Description |
|---|---|---|
| A0A4S4DMA6 | E-Value: 1.926e-82, PID: 65.09 | BHLH domain-containing protein {ECO:0000259|PROSIT... [more] |
| A0A7J7HE48 | E-Value: 4.844e-81, PID: 64.15 | BHLH domain-containing protein {ECO:0000259|PROSIT... [more] |
| A0A2R6PJJ1 | E-Value: 4.928e-75, PID: 62.96 | (Transcription factor bHLH147 like {ECO:0000313|EM... [more] |
| A0A7J0GSY6 | E-Value: 1.453e-74, PID: 64.85 | (Basic helix-loop-helix (BHLH) DNA-binding superfa... [more] |
| A0A5J5AJH6 | E-Value: 1.517e-74, PID: 66.84 | (Uncharacterized protein {ECO:0000313|EMBL:KAA8531... [more] |
| A0A5J5A8F1 | E-Value: 1.749e-74, PID: 66.84 | (Uncharacterized protein {ECO:0000313|EMBL:KAA8527... [more] |
| A0A834HDQ1 | E-Value: 3.881e-74, PID: 62.50 | (Uncharacterized protein {ECO:0000313|EMBL:KAF7151... [more] |
| A0A7J0GKY0 | E-Value: 1.393e-73, PID: 65.46 | (Sequence-specific DNA binding transcription facto... [more] |
| A0A5N6RC87 | E-Value: 1.488e-73, PID: 64.82 | (Uncharacterized protein {ECO:0000313|EMBL:KAE8076... [more] |
| A0A5B6YXD1 | E-Value: 1.762e-73, PID: 65.50 | (Uncharacterized protein {ECO:0000313|EMBL:MPA3642... [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. |