DCAR_027544

Resource Type: 
Polypeptide
Name: 
DCAR_027544
Identifier: 
DCAR_027544.mRNA-protein
Sequence: 
MSAGVYKFWNCTLYLFLICHAQIIPTSTATVKGNETDHLALLAFKATIIH
DPQGAFSSWNMSLNFCSWAGITCSKQHKRVTSINLASKGFVGSLPSDIGN
MSFLTEIVLTNNSLQGTIPQEVDHLFRLKVLSLGRNALEGNIPDTLGQVN
RLVILELFSNNLSGMIPNSVFNLSSLNVFNLANNQLQGSIPSDFGLTHHN
IQKIQLSDNRLSGNIPVSLSNASKLQVIHLQFNNFSGPISVDFGRLLYLQ
NLSLEYNNFGLGEQGDLKFIDSLVNCRSLKILKLGANNLQGSLPRSIANL
SIKLTMISLADNWISGSIPPDISKFINLIFLSLEHNNFTGIIPPEITQLG
KLQRVLLSNNRLTGNIPASIGNLSMLDEVHLENNELNGTIPPSFGNCPML
VLLDLSQNNLSGTIPNEFFHVSPFSIKLNLSQNHLVGSLPAGIGGLDTIV
ELDISENEFSGFFPTELGRCITLDTLYMQGNFFRGHISHSMRNLRGMQNL
DLSRNNLSGEIPDFFELPLKYLNLSWNHLEGEVHTKGVFANASEFSIVGN
KELCGGIPELRLPRCSSDSDRSHKHKRSWVQDLFMIGFILVLLIVGYHLL
PRGKKTEPPAVSIRPISVLPIRLSYKILHQATDGFSRANLVSEGGFGSVY
KGELGPEYNGKAVAIKVFNQEATNSFSTECEAQQHIRHRNIVKIRSTSSS
TAKKGKIFRAIVYDFMENGSLDRWQHLTCRTSPDELSMPQILNLKNRINI
AIDVASALDYLHNQLDYPLIHCNLSPSNIFLDTEMSAYVSNFGLAKFLID
RRIFNGFAGPSEYAPPEYYQGSMVSTKGDVYSYGIILLEMLTGKKITGPS
FHGSFKLQNFVSSVLSSGVNDVIDPFNLQELSTYDAAKANDCLVMLLGIG
VRCAQESPKFRPDIKDTLRVLETIRSFFEANTGCTQTYAIGSLQAAVSMA
LRNRRSLLWNRLEVSEMPSPNLGETNSGRTDWNVATARQLLDPFPQMAPN
LATVSYMDLHKATNGFSSANLVGAGGFGSVYKGTFNQGYVHLLLRDSEIV
DEIGIAVAIKVFNLQRRGAVRSFNTECQILNNIDHKYLVKLIATCTSVDQ
DGHDFRAILFEFMDHGKYGLGCKMTTKGDTYSFGILLLEMLTGKKPTHRM
FRGGLTLHNFVSLALPDNVFNITDTLMKIKCFASGQYRLYSDVCYRKFAS
CSLDGSKKQEISTLEQCCRLEVSEMPSPNLGETNSGRTDWNVATARQLLD
PFPQMAPNLATVSYMDLHKATNGFSSANLVGAGGFGSVYKGTFNQGYVHL
LLRDSEIVDEIGIAVAIKVFNLQRRGAVRSFNTECQILNNIDHKYLVKLI
ATCTSVDQDGHDFRAILFEFMDHGKYGLGCKMTTKGDTYSFGILLLEMLT
GKKPTHRMFRGGLTLHNFVSLALPDNVFNITDTLMKSTTNYIVNLHLLVE
FSDNFSPTKCMHNNLHQSSALKTSHRMRAAGANRYWTHVISLFLISTSQA
AASSGNETDQLALLAFKAKISHDPLGAFSSWNMSLHFCLWEGITCSQRHQ
RVIILDLSSKGLVGSLSPHIGNMSFLTKLVLYNNNLRGLIPPEVDRLSRL
QVLSLGRNALEGNIPDTLGRLNRLVILELFSSKLSGMITTFFNLSSLKVY
NLANNQFQGSIPSEFGLAYPNLQKIQLSDNNLSGTIPVSLSNASTLQVID
LQFNRFSGPTLVDFGRLPYLQKLGLANNNLGVGEHGDLSFFDSLVNCSSL
KILEVGANNLQGSLPCSFVNLSTELTMISLADNQIFGSIPSEICKFTNLI
FLSLGGNKFTGMIPPGIVKLRKLQRIVLSNNRLTGSIPASIGNLSMLDEV
HLENNELNGTIPSSFGNCPMLVLLDLSQNNLSGTIPNQFFHVSPFSVKLN
LSQNHLVGSLPAGIGALKTLVKLDVSENELSGLIPTELYDCSALESLYMR
GNFIQGFKSQPVKKLRALQNIDLSRNNLSGKIPDFFETLHLKYLNLSWNN
LEGDVPKKGLFANASAYSIVGNRLCGGIPELQLPRCSSYSPAYQIIVVLL
GLVFILLIFTILLHIYANMVLRSVLNRPISVSPITLSYKQLHQATNGFSK
TNLVSKGASGLVYKGKIGPQYNKRAVAIKVFNEEATNCFITEIEALQNIH
HRNIVKIMSICSTIVENRGFKAIVYNVTEHRSLEWWLHSKKYCLRSSMST
KGDVYSYGLILLEMLTGKKTTDPMFNEGYKLQNFVSSALSDGVKDIIDPV
NLHELSRDAAAHAEDSLSMLFNIGVKCTLEMPQFRPDIRDTLSMLKTVRI
NFKANHTTEAYARTSSLASVIMAQRNMKSLPLYGITKMAPNSRSMSTLSS
VVVSYVDLHKATNGFSLTNLVGAGGYGSVYKGRFLLGNSGLEDGTGTAVA
IKVFNLQRRGAVKSFNTEYGTLKNIHHPNLVKTITTCTSVDKEGGAFRAI
LYEFMDHGKYGLGCKMTTKGDTYSFGILLLEMLTRMKPTHRMFRKGLNLH
NFVWMAFPNNIVDITDPLMKIRSSANEGECLTRLFNIGEFSNKHPHQTAA
LETSYRMRAAGVNRYWTHVISLFLISTSAAAAASGGNETDQLALLAFKAK
ISDDPLGVFSSWNMSLHFCLWEGITCNKQHQRVVSLNLSSTGLVGSLCPD
IGNMSFLREIDLYNNSLQGPIPQEVDRLFRLKVLSLGRNDLEGKIPGTIG
RLKSLFFVDISSNELSGMIPTSIFNISSLSSFNLASNQLEGSIPSDIGLT
LPNLKLIRLSYNKLTGSIPASLSNVSKLQAIEFQSNNLRGPVSVDFGRLP
YLQLLRLSYNNLGSGEEGNLSFLDPLTNCSRLLILELESNNFQRSLPSSI
ANLSTTLQIISLAYNQISGSIPSGIGNCISLILLSLQGNKLTGIIPSEIA
RLGKLQRVILSNNMLSGSIPASIGNLSLLDEIHLEDNQLQGTIPAGFGNC
PMLVFLDLSRNNLSGTIPRNLFSISPFSVKLNLSRNHLVGSLPAAIGALG
TVVELDVSENEFSGFIPVELGRCISLSSLYMQGNFIQGYIPESLTNLRGL
QYIDFSRNKLSENIPDFFGDLIYVEYLNLSCNNLAGKVPMIGVFSNASAF
SIVGNKKLCGGIPELRLKKCSKKYIGTYNQIMAWGQVFILIGSIQDLLII
SCVFMSWHRRKRREQLRYSASNVMISPNKMSYELLRQATKGFSRTNLVSE
SGFGLVYKGKLDLKYIGIPEGEKAAIAVKIFNTLNEEAANCFITECETLK
NIRHRNIVRIISTCENHKFKAIVYDFMKNGSLEGWLHSTKYGLGSMVSTK
GDVYSYGIILLEMLTGKKITDPMFQNGFKLQNFVSNALSDGIKGIVNPVN
LFELTRENAAEAEDCLSILFNIGLKCALDLPQFRPDISDILSMLETVRII
FKMPPDSRSMSISPSVTLSFMDIHKATNGLSSTNLLGAGGFGSVYKATFH
QENVRLLLRNSGIEDRIGTAVAIKVFNLQRRGAARSFKTEYKILRNISHM
NLVKVITACTSKDLEGDSEPVKMFDRTANLANNQIINYKCDSSEKWLVLI
GIAPGSPEISHRYSLIHVITKLGLLYVYDLKTAAALNNPKLAVDLSGGNL
PVAENLVGYTPHDYLFLLQTILRSDSRGAVKFALMMAHMEGGCPVDYNII
TDLFIEVPTITILSGNERDQQALLAFRAKIFNDPLGVFSSWNMSLHFCSW
VGITCSKQHKRVTSINLSSKALVGSLSPDVGNMSFLSEIILYDNHLQGAI
PQEVDRLFRLKVLNLGQNAFEGSIPNTLGRLNRLVILKLFSNKLSGVIPT
SVFNLSSLNVFNLANNQLQGSIPSGFGSTLPNLQKIQLSDNKFSGSIPMS
LYNASKLQTIDLQFNNFSGPISVDCRSLKILELGANNLQGSLSRSIANLS
VELTMISLADNQISGSIPPDISKFINLIFLSLEGNNFTGIIPPEITELGK
LQRVLLSNNRFSGNIPASIGNLSMLDEIHLQNNDLNGMIPPSFGNCPMLV
LLDLSQNNLSGTIPNELFQVTPFSVKLNISRNHLVGSLPAGIGALKTLVE
LDISENEFAGFIPAELGDCVTLDSLYMQGNFLQGNISQSMKKLRGLRNVD
LSRNNLSGKIPDFFENLSLKYLNLSWNHFKGELHTKGVFANASAFSIVGN
KGLCGGIPELRLRRCSTHKMSWVQILIMIGSIQVLLVVGCLLWLRRKKTE
TRAVSIGPASVFLIRLSYELLHQATDGFSRANLVSEGGFGSVYKGELGAQ
YSENAVAIKVFNEGAANNFNTECGALQNIRHRNIVKIRSTCKSIERSGKE
FTAIIYDFMENGSLDSLEMLTGKKITDPMFDRSYKLQNFVSNALSDRVID
VIDPFNLHELSRYDAAMAMDCLEMLLDIGVRCALESPQFRPDIKDTLSIL
ETVRRVFEDNTGGTETYTTGSFQDAVLVAQINSRSLPWNRLEVPEVPSRN
LVERNSGGADRNVAATRQSMDPSPQMAPNSVTVSYTRQLRDPSPQMAPNL
ATVSYMDLHKATNGFSSANLVGAGGFGSVYKGTFDQEYVRLLLGDSGIED
EIGIAIAIKVFNLQRRGAVKSFNTEYQTLNDIDHTYLVKLITTCTSVDQD
GHDFRAILFEFMDQGSLEMWLHPTYKKYGLGCKMTTKGDTYSFGILLLEM
LTGKKPTNRMFRGGLNLHNFVSLSLPDDVIKITDPLMKVMTSANKGDDKR
VEDCLTRMYSIGLACSKTSAKDRPDMRDNSELGFKRERERGFCQQGGNLF
ITESQARVQISSFFQGFDLLKMDDEFKVLRFNWRGKIVDIRVEIDKCTLL
DVVMDYEAKGKEEGVKLDYHFPTFYYRYKDDQFQLVVDKDMMTMFKRCAE
KALIPIAVGTTIKPSPIHKLVLNLRRSNEAKHPPAAAIDNVVENVQENDV
GLEDLEDNSVATLYFPARMAGGGPINSGSGKAYPGELTTYIMLTCIIAAM
GAAMGGLIFGYDIGISGGVTSMDPFLKKFFPSLYRKQKADHSQNQYCKFD
SQILTMFTSSLYLAALCSSVVASWVTRRLGRKLSMLSGGSLFCAGALING
FAQDVAMLIIGRILLGFGIGFANHAVPLYLSEMAPYEYRGGLNIMFQLSI
TVGILVANVFNYAFDKIEGGWGWRLSLGGAVVPAVIMIAGSLYLPETPNS
LIENGKQDKAKKQLIKIRGVDDVEEEFNDLIAASEAEDPWRNLWQPKYRP
QLVMGILIPFFQQVAGINVIMFYAPVLFKTIGFGGDASLVSAVITGGDAE
LM*
Sequence Length: 
5253
Sequence Checksum: 
a8147651f26f33af064394aacc81edf1
View location in JBrowse: 
DCARv2_Chr8:21944631..21999259+
Organism: 
Daucus carota subspecies sativus
Relationship: 
There is 1 relationship.
Relationships
The polypeptide, DCAR_027544, derives from mRNA, DCAR_027544.
Blast Results: 
The following BLAST results are available for this feature:
BLAST of DCAR_027544 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
Position :
0
Zoom :
x 1
500100015002000250030003500400045005000SequenceA0A5B6Z2X4A0A7N2MQI2A0A7N2ME52A0A2N9IL34A0A4S4D901A0A7N2LT67A0A6J1BCB5A0A4S4DKF0F6HKT0A0A2H5PY30
Match NameStatsDescription
A0A5B6Z2X4E-Value: 6.958e-178, PID: 44.20(Putative LRR receptor-like serine/threonine-prote... [more]
A0A7N2MQI2E-Value: 6.429e-174, PID: 44.92Protein kinase domain-containing protein {ECO:0000... [more]
A0A7N2ME52E-Value: 2.571e-174, PID: 43.83Protein kinase domain-containing protein {ECO:0000... [more]
A0A2N9IL34E-Value: 3.312e-177, PID: 43.61Protein kinase domain-containing protein {ECO:0000... [more]
A0A4S4D901E-Value: 8.455e-177, PID: 43.19Protein kinase domain-containing protein {ECO:0000... [more]
A0A7N2LT67E-Value: 1.607e-174, PID: 43.63Protein kinase domain-containing protein {ECO:0000... [more]
A0A6J1BCB5E-Value: 2.623e-173, PID: 44.12(LOW QUALITY PROTEIN: probable LRR receptor-like s... [more]
A0A4S4DKF0E-Value: 6.590e-179, PID: 44.35Protein kinase domain-containing protein {ECO:0000... [more]
F6HKT0E-Value: 2.324e-164, PID: 41.56(Uncharacterized protein {ECO:0000313|EMBL:CCB5550... [more]
A0A2H5PY30E-Value: 6.498e-178, PID: 42.61Protein kinase domain-containing protein {ECO:0000... [more]

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Analysis: 
NameDescription
Carrot Genome Assembly DCARv2

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
Authors' original naming scheme: Sequences with DCARv2 prefix are the original assembly as submitted to NCBI. These are labelled DCARv2_Chr1 through DCARv2_Chr9 for the chromosome pseudomolecules, DCARv2_MT and DCARv2_PT for the organellar assemblies, DCARv2_B1 and up for unincorporated superscaffolds, DCARv2_S26.1 and up for unincorporated scaffolds, and DCARv2_C10542132 and up for unincorporated contigs. A file with sequences using this naming scheme can be downloaded from the File: link below.
These sequences can be viewed in JBrowse here.

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
DCAR peptide blastp to SwissProt and TrEMBL without DCAR

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.
DCAR V1.0 Gene Prediction

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.