MLAIFHKAFAHPPEELNSPASHKQKPKLPEETLQQFLSVHPTNTFSMTFA
QSAVLAYVKPDHVTMLRHQRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSK
GTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTAL
GSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGL
MNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEW
DTSY*
| Relationships |
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| The polypeptide, DCAR_020983, derives from mRNA, DCAR_020983. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A251U7Y1 ((Putative aluminum induced protein with YGL and LRDR motifs {ECO:0000313|EMBL:OTG19460.1}))
HSP 1 Score: 467.618 bits (1202), Expect = 8.252e-167
Identity = 219/254 (86.22%), Postives = 235/254 (92.52%), Query Frame = 0
Query: 1 MLAIFHKAFAHPPEELNSPASHKQKPKLPEETLQQFLSVHPTNTFSMTFAQSAVLAYVKPDHVTMLRHQRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEWDTSY 254
MLAIFHKAFAHPPEEL SPA HK +PKLPEETLQ+FLSVHPTNTFSMTF +AVLAYVKP+ + +QRLF FDDIYCLF+GSLNNLCSQIKQYGLSK TNEAMFVIEAYRTLRDRGPYPADQVIKD+EGSFAFVVYDSK G VFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLM+FEHPMNK++AMPRVDSEGVMCG+NFK+D YSRVNSIPR GS++NWT+WD Y
Sbjct: 1 MLAIFHKAFAHPPEELKSPAKHKTQPKLPEETLQEFLSVHPTNTFSMTFGDAAVLAYVKPN-LNYSVNQRLFTSFDDIYCLFMGSLNNLCSQIKQYGLSKNTNEAMFVIEAYRTLRDRGPYPADQVIKDLEGSFAFVVYDSKTGTVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMSFEHPMNKLKAMPRVDSEGVMCGSNFKVDTYSRVNSIPRRGSEANWTQWDDHY 253
Match: A0A2J6LHK4 (DUF3700 domain-containing protein {ECO:0000259|SMART:SM01172})
HSP 1 Score: 462.996 bits (1190), Expect = 5.944e-165
Identity = 219/253 (86.56%), Postives = 236/253 (93.28%), Query Frame = 0
Query: 1 MLAIFHKAFAHPPEELNSPASH--KQKPKLPEETLQQFLSVHPTNTFSMTFAQSAVLAYVKPDHVTMLRHQRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEWD 251
MLAIFHKAFAHPPEELNSPA+H ++PKLPEETL++FLSVHPTNTFSMTF +A LAYVKPD + HQRLF FDDIYCLF+GSLNNLCSQIKQYGLSK TNEAMFVIEAYRTLRDRGPYPADQVIKD+EGSFAFVVYDSK+G VFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLM+FEHPMNK++AMPRVDSEGVMCGANFK+D YSRVNSIPR GS++NWT+WD
Sbjct: 1 MLAIFHKAFAHPPEELNSPAAHHCTKQPKLPEETLEEFLSVHPTNTFSMTFGDAAALAYVKPDRPYSV-HQRLFTAFDDIYCLFMGSLNNLCSQIKQYGLSKNTNEAMFVIEAYRTLRDRGPYPADQVIKDLEGSFAFVVYDSKSGTVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMSFEHPMNKIKAMPRVDSEGVMCGANFKVDTYSRVNSIPRRGSETNWTQWD 252
Match: A0A6S7N3W0 (DUF3700 domain-containing protein {ECO:0000259|SMART:SM01172})
HSP 1 Score: 462.996 bits (1190), Expect = 5.944e-165
Identity = 219/253 (86.56%), Postives = 236/253 (93.28%), Query Frame = 0
Query: 1 MLAIFHKAFAHPPEELNSPASH--KQKPKLPEETLQQFLSVHPTNTFSMTFAQSAVLAYVKPDHVTMLRHQRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEWD 251
MLAIFHKAFAHPPEELNSPA+H ++PKLPEETL++FLSVHPTNTFSMTF +A LAYVKPD + HQRLF FDDIYCLF+GSLNNLCSQIKQYGLSK TNEAMFVIEAYRTLRDRGPYPADQVIKD+EGSFAFVVYDSK+G VFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLM+FEHPMNK++AMPRVDSEGVMCGANFK+D YSRVNSIPR GS++NWT+WD
Sbjct: 1 MLAIFHKAFAHPPEELNSPAAHHCTKQPKLPEETLEEFLSVHPTNTFSMTFGDAAALAYVKPDRPYSV-HQRLFTAFDDIYCLFMGSLNNLCSQIKQYGLSKNTNEAMFVIEAYRTLRDRGPYPADQVIKDLEGSFAFVVYDSKSGTVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMSFEHPMNKIKAMPRVDSEGVMCGANFKVDTYSRVNSIPRRGSETNWTQWD 252
Match: A0A2U1KL04 ((Aluminum induced protein {ECO:0000313|EMBL:PWA37466.1}))
HSP 1 Score: 461.07 bits (1185), Expect = 3.172e-164
Identity = 220/253 (86.96%), Postives = 233/253 (92.09%), Query Frame = 0
Query: 1 MLAIFHKAFAHPPEELNSPASH---KQKPKLPEETLQQFLSVHPTNTFSMTFAQSAVLAYVKPDHVTMLRHQRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEW 250
MLAIFHKAFAHPPEELNSPAS K KPKLP ETL +FLSVHPTNTFSMTF +SAVLAYVKP+ R+QRLF FDDIYCLF+GSLNNLCSQIKQYGLSK TNEAMFVIEAYRTLRDRGPYPADQVIKD+EGSFAFVVYDSKAG VFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSE GLM+FEHPMNK++AMPRVDSEGVMCGANFK+D YSRVNSIPR GS++NWT+W
Sbjct: 1 MLAIFHKAFAHPPEELNSPASKQTSKHKPKLPTETLNEFLSVHPTNTFSMTFGESAVLAYVKPES---YRNQRLFTAFDDIYCLFMGSLNNLCSQIKQYGLSKNTNEAMFVIEAYRTLRDRGPYPADQVIKDLEGSFAFVVYDSKAGTVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEDGLMSFEHPMNKIKAMPRVDSEGVMCGANFKVDTYSRVNSIPRRGSEANWTQW 250
Match: A0A124SE67 (DUF3700 domain-containing protein {ECO:0000259|SMART:SM01172})
HSP 1 Score: 460.685 bits (1184), Expect = 3.578e-164
Identity = 217/255 (85.10%), Postives = 236/255 (92.55%), Query Frame = 0
Query: 1 MLAIFHKAFAHPPEELNSPAS-HKQKPKLPEETLQQFLSVHPTNTFSMTFAQSAVLAYVKPDHVTMLRHQRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEWDTSY 254
MLAIFHKAFA+PPEEL SPAS H KPKLPEETL++FLSVHPTNTFSMTF +AVLAYVKPD + HQR+F FDDIYC+F+GSLNNLC+QIKQYGLSK T+EAMFVIEAYRTLRDRGPYPADQVIKD+EGSFAFVVYDSK+G VFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLM+FEHPMNK+RAMPRVDSEGVMCGANFK+D Y+RVNSIPR GS++NWT+WD Y
Sbjct: 1 MLAIFHKAFANPPEELKSPASNHSNKPKLPEETLEEFLSVHPTNTFSMTFGDAAVLAYVKPDRPYSV-HQRMFTAFDDIYCVFMGSLNNLCAQIKQYGLSKNTDEAMFVIEAYRTLRDRGPYPADQVIKDLEGSFAFVVYDSKSGTVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMSFEHPMNKIRAMPRVDSEGVMCGANFKVDTYTRVNSIPRRGSEANWTQWDNHY 254
Match: A0A6I9U7C7 ((stem-specific protein TSJT1-like {ECO:0000313|RefSeq:XP_011069390.1, ECO:0000313|RefSeq:XP_011095236.1}))
HSP 1 Score: 459.914 bits (1182), Expect = 1.074e-163
Identity = 214/256 (83.59%), Postives = 236/256 (92.19%), Query Frame = 0
Query: 1 MLAIFHKAFAHPPEELNSPASHK--QKPKLPEETLQQFLSVHPTNTFSMTFAQSAVLAYVKPDHVTMLRH-QRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEWDTS 253
MLAIFHKAFAHPPEELNSPASHK +KPKLPEETL +FLS HPTNTFSM+F +AVLAYV+PD + L H QRLFCG+DDIYCLF+GSLNNLC+QIKQYGLS+ NEAM VIEAYRTLRDRGPYPADQVIK++EGSFAFVVYDSK G VFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFP GC+FHSE GLM+FEHPMNK+RAMPRVDSEGVMCGANFK+D+YSRVNSIPRVGS++NW W+++
Sbjct: 1 MLAIFHKAFAHPPEELNSPASHKVAKKPKLPEETLDEFLSSHPTNTFSMSFGDTAVLAYVRPDRCSFLHHNQRLFCGYDDIYCLFMGSLNNLCAQIKQYGLSRNANEAMLVIEAYRTLRDRGPYPADQVIKELEGSFAFVVYDSKVGTVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPAGCIFHSEAGLMSFEHPMNKLRAMPRVDSEGVMCGANFKVDLYSRVNSIPRVGSEANWAPWNSN 256
Match: A0A5N6NWJ3 (DUF3700 domain-containing protein {ECO:0000259|SMART:SM01172})
HSP 1 Score: 456.447 bits (1173), Expect = 2.232e-162
Identity = 216/256 (84.38%), Postives = 234/256 (91.41%), Query Frame = 0
Query: 1 MLAIFHKAFAHPPEELNSPASH--KQKPKLPEETLQQFLSVHPTNTFSMTFAQSAVLAYVKPDHVTMLRHQRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEWDTSY 254
MLAIFHKAFA+PPEEL SP +H ++PKLPEETL +FLSVHPTNTFSMTF +AVLAYVKPD + QRLF FDDIYCLF+GSLNNLC+QI+QYGLSK TNEAMFVIEAYRTLRDRGPYPADQVIKD+EGSFAFVVYDSKAG VFTALGSDGGVKLYWGIAADGSVVISDDLEVIK+GCAKSFAPFPKGCMFHSEGGLM+FEHPMNK+RAMPRVDSEGVMCGANFK+D YSRVNSIPR GS++NWT+WD Y
Sbjct: 1 MLAIFHKAFANPPEELKSPVAHHVSRQPKLPEETLNEFLSVHPTNTFSMTFGDAAVLAYVKPDRGYSV-DQRLFTAFDDIYCLFIGSLNNLCAQIRQYGLSKNTNEAMFVIEAYRTLRDRGPYPADQVIKDLEGSFAFVVYDSKAGTVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKSGCAKSFAPFPKGCMFHSEGGLMSFEHPMNKIRAMPRVDSEGVMCGANFKVDTYSRVNSIPRRGSEANWTQWDDHY 255
Match: A0A2G9HYN2 (DUF3700 domain-containing protein {ECO:0000259|SMART:SM01172})
HSP 1 Score: 451.825 bits (1161), Expect = 1.383e-160
Identity = 211/254 (83.07%), Postives = 235/254 (92.52%), Query Frame = 0
Query: 1 MLAIFHKAFAHPPEELNSPASHK--QKPKLPEETLQQFLSVHPTNTFSMTFAQSAVLAYVKPDHVTMLRH-QRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEWD 251
MLAIFHKAFAHPPEELNSPAS K +KPKLPEETL++F+S HPTN+FSM F +AVLAYV+P H + LRH QRLFCG+DDIYCLF+GSL+NLC+QIKQYGLS+ NEAM VIEAYRTLRDRGPYPADQVIKD+EGSFAFVVYDSK G VFTALGSDGGV+LYWGIAADGSVVISDDLEVIKAGCAKSFAPFP GC+FHSE GLM+FEHPMNK+RAMPRVDSEGVMCGANFK+D+YSRVNSIPRVGS++NW +W+
Sbjct: 1 MLAIFHKAFAHPPEELNSPASGKGSKKPKLPEETLKEFISSHPTNSFSMGFGDAAVLAYVRPHHHSFLRHNQRLFCGYDDIYCLFMGSLDNLCAQIKQYGLSRNANEAMLVIEAYRTLRDRGPYPADQVIKDLEGSFAFVVYDSKVGTVFTALGSDGGVRLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPPGCIFHSEAGLMSFEHPMNKLRAMPRVDSEGVMCGANFKVDLYSRVNSIPRVGSEANWADWN 254
Match: A0A2I4H4H1 ((stem-specific protein TSJT1-like {ECO:0000313|RefSeq:XP_018851056.1}))
HSP 1 Score: 451.055 bits (1159), Expect = 2.814e-160
Identity = 216/254 (85.04%), Postives = 233/254 (91.73%), Query Frame = 0
Query: 1 MLAIFHKAFAHPPEELNSPASHK--QKPKLPEETLQQFLSVHPTNTFSMTFAQSAVLAYVKPDHVTMLRHQRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEWDT 252
MLAIFHKAFAHPPEELNSPAS+ +KPKLPEETL FLS+HP NT SM+FA +AVLAYV+PD L HQRLFCGF+DIYCLFLGSLNNL S IKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKD++GSFAFVVYDSK G VF ALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFP GCMFHSEGGLM+FEHPMNK++AMPRVDSEG MCGANFK+D Y+RVNSIPRVGS+SNWT+WD+
Sbjct: 1 MLAIFHKAFAHPPEELNSPASYNGTKKPKLPEETLNDFLSLHPHNTSSMSFADAAVLAYVRPDPPCQL-HQRLFCGFEDIYCLFLGSLNNLFSLIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDLDGSFAFVVYDSKTGTVFAALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPTGCMFHSEGGLMSFEHPMNKVKAMPRVDSEGAMCGANFKVDKYTRVNSIPRVGSESNWTQWDS 253
Match: A0A7J6HZ33 (DUF3700 domain-containing protein {ECO:0000259|SMART:SM01172})
HSP 1 Score: 448.743 bits (1153), Expect = 2.336e-159
Identity = 213/252 (84.52%), Postives = 232/252 (92.06%), Query Frame = 0
Query: 1 MLAIFHKAFAHPPEELNSPASHK--QKPKLPEETLQQFLSVHPTNTFSMTFAQSAVLAYVKPDHVTMLRHQRLFCGFDDIYCLFLGSLNNLCSQIKQYGLSKGTNEAMFVIEAYRTLRDRGPYPADQVIKDMEGSFAFVVYDSKAGKVFTALGSDGGVKLYWGIAADGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMNFEHPMNKMRAMPRVDSEGVMCGANFKLDVYSRVNSIPRVGSQSNWTEW 250
MLAIFHKAFAHPPEELNSPAS+K KPKLPEETLQ FLS HP NTFSMTF +AVLAYV+PD L +QRLFCGF+DIYCLFLG+LNNLCS KQYGL+KGTNEAMFVIEAYRTLRDRGPYPADQV+K+++GSFAFVVYDSK G VFTALGSDGGV+LYWGIA DGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLM+FEHPMNK++AMPRVDSEGVMCGANFK+D Y+RVNSIPRVGS++NW EW
Sbjct: 1 MLAIFHKAFAHPPEELNSPASYKGSSKPKLPEETLQDFLSHHPQNTFSMTFGHAAVLAYVRPDRPFSL-NQRLFCGFEDIYCLFLGNLNNLCSLNKQYGLTKGTNEAMFVIEAYRTLRDRGPYPADQVVKELDGSFAFVVYDSKTGSVFTALGSDGGVQLYWGIAGDGSVVISDDLEVIKAGCAKSFAPFPKGCMFHSEGGLMSFEHPMNKVKAMPRVDSEGVMCGANFKVDKYTRVNSIPRVGSETNWVEW 251
| Match Name | Stats | Description |
|---|---|---|
| A0A251U7Y1 | E-Value: 8.252e-167, PID: 86.22 | (Putative aluminum induced protein with YGL and LR... [more] |
| A0A2J6LHK4 | E-Value: 5.944e-165, PID: 86.56 | DUF3700 domain-containing protein {ECO:0000259|SMA... [more] |
| A0A6S7N3W0 | E-Value: 5.944e-165, PID: 86.56 | DUF3700 domain-containing protein {ECO:0000259|SMA... [more] |
| A0A2U1KL04 | E-Value: 3.172e-164, PID: 86.96 | (Aluminum induced protein {ECO:0000313|EMBL:PWA374... [more] |
| A0A124SE67 | E-Value: 3.578e-164, PID: 85.10 | DUF3700 domain-containing protein {ECO:0000259|SMA... [more] |
| A0A6I9U7C7 | E-Value: 1.074e-163, PID: 83.59 | (stem-specific protein TSJT1-like {ECO:0000313|Ref... [more] |
| A0A5N6NWJ3 | E-Value: 2.232e-162, PID: 84.38 | DUF3700 domain-containing protein {ECO:0000259|SMA... [more] |
| A0A2G9HYN2 | E-Value: 1.383e-160, PID: 83.07 | DUF3700 domain-containing protein {ECO:0000259|SMA... [more] |
| A0A2I4H4H1 | E-Value: 2.814e-160, PID: 85.04 | (stem-specific protein TSJT1-like {ECO:0000313|Ref... [more] |
| A0A7J6HZ33 | E-Value: 2.336e-159, PID: 84.52 | DUF3700 domain-containing protein {ECO:0000259|SMA... [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. |