DCAR_022143 | CarrotOmics

Resource Type:

Gene

Organism:

Daucus carota subspecies sativus

Name:

DCAR_022143

Identifier:

DCAR_022143.gene

Locus Tag:

DCAR_022143

Publication:

Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J, Bowman M, Iovene M, Sanseverino W, Cavagnaro P, Yildiz M, Macko-Podgórni A, Moranska E, Grzebelus E, Grzebelus D, Ashrafi H, Zheng Z, Cheng S, Spooner D, Van Deynze A, Simon P. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.. Nature genetics. 2016 06; 48(6):657-66.

Relationship:

There are 2 relationships.
Relationships
The mRNA, DCAR_022143, is a part of gene, DCAR_022143.
The genetic_marker, MK005218 K2662, is adjacent to gene, DCAR_022143.

Analysis:


Name	Description
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 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.

Transcripts:


Transcript Name	Identifier	Type	Location
DCAR_022143	DCAR_022143.mRNA	mRNA	DCARv2_Chr6:16258656..16265271

Sequence:

ATGGCCACCGGAGATCTGGATCTCATGCATCCCCCTCCCCCTCCCCCTCC
CGCCGACTCCGGCGCCGACGCCGGAAAAGAAGCGTGTTCGATTTGCCTGG
ACGTTGTCTCCGATAACGCCGATCGATCCTTCGCCAAGCTTCATTGCGGC
CATCTCTTTCATCTCGGTACCCATTTTCTTCATTCCTTTTATTTCTTATC
GTTATTGTTTTTCTGTTTGTTTATGTATCTATTTATCTCGAGCTCGTGCG
ATTTTTTCGTTCACTATGATGTAAAGTAGTAGCTGTTGATTGTTCTTTGA
TTCTTGTATACTATGCATCACTTCGAGCTTAATGCTGCTGACGTATTTAT
AATCGAATTGTATTTAAGGGATTTTTTCCGGTTTTTTTGTTCTGTCTTGA
GTTGTATGTATGTGTCCGTATTAGGTCAATTAATTGCAATTGAGTGTCTA
TAAGTGTTATATGCTGTCACAGCCTTCTTTCTCGCACCAGAATTGATTGC
TATGTCTTTGGCTTTGTCGTGCTACTCTTTTTCAACTTAATAACACCTTA
TCCTAGACTCCACTATGGTACATATGCAAACTCGAACTCTGCCACCATGA
AACCCCCTATGTCATGGAAAGCCCAAGTTTTTCAGTTGTTATTTAGCTAT
GGACTGTTTTTATTTCCATGTTGTTTTTAGGACCACTAATGGAGTATATC
ACGTGGAGTTGCAAAAGGTGGTTTGTTCAAGCATTTATTGGTGACCGTAC
ATATTTTTTGTCACAAGTATCTAGGCCATGAATCTAAGGAAAAAAGTTCC
CTTGTTAGTCGATTTCATTTGCCATGTAATCATGACAATGTTGGTAGTCC
TGAACATTGTAATGTTTGCGTATTGTAAGAGTCATCATTTTTCTTTTTAA
AAGATATTTTTAAATCTTTGCATTCATTACACTATTTTTATGCCAATGTC
TGAGGGCCTGCAAATATTCCCTATATGAATGAAAATCGTTATTATCTTTT
ATTGGTTGATCTGTACTTAAATTACTCTTGCATTACTGCCATAAAGTTGG
GAATTATACCTTCCAAATTGCAGTGCATCTTTCTGGTAGGCTGCCAATAC
CTCTATTATATAGCATATCACATTTTCGAGTAATATTAGTAAGGTGTAAC
TATCCAAAATTGAGGACATTCAGATGATTTTCCGTAGTTACCCACATACA
ACTTTGGAAGGTTTGAAATACCATCTGGTTGGTGCATCTTTCTTGGGTAT
TCGACCACTGAAAGTATTACAATGATATTTTCAACGGTCAAGTTTGTTAA
TCACAATGTTATGTATGCTTCATTAAAAGTGTCAAGCTGCTGGAAAATTG
AAAATGGAATTGGTCTATATGTATATGTGATCTTGTACAGATGACACATT
GTTTTTTAACCTATATGGTATTTCTTGGCCAAAATCCAATATCATGGTAA
TCATGATAAACAAAAACAAATTGCTGTCTTAAGGCTACGCCTTGGTACAT
GCTTGGTGGATTCAACATTCGTTTGGAAAATCGGATTTTTGCTCTGCCAG
TTGTGTTATTTTGTGATGACATCGGTGCCACAGGTCTTTTGTTGCATCAT
GTGCAACATTTTAGAATGAAACATATATCAGTTGATCTACACTTTATAAT
CGATGCAGTTGGTATAGGTTTTTTTTGTTGTTTCCTATGTGAATAGTCAA
TAACATCGATTAGCTTGCTGATGCGATGGCGAAACTGCTCCCCTGTATTC
TCATTGCAGATGGAACATTGTTTTGCAGGGGATTATCAGACTTATTAATA
TTATATTGACATTCGTACTATTTTTATGTGTAAACATTCATAATTTAGTC
CTGCCATATTCTAGCAATTTGAGCTGAAGCTTAAATCCACTACTATAAGA
AGAAATACTTTACCCCCCATTCTGCTCATTTTTTCTTACAGTTCTCATTG
TAGGAAGTTTTTAATACCATAGTTTTTCGCTCTTATTTCCTACCTCCATT
TTCCTCGTTAAAATTTTATTCCCAACTTTGCCATTTCAGTTCCGCAGACC
AAACATAACAATATTATATATAAATTACTAGCTAACTATTCTTTGGTTTT
TTTCTGAGGAATACACTTTAAGACTACATGATCTCATCCGTGTATCTCTT
TTATCATGTATACTAGATGCTCCCGTGCTGGATAATTGTGGAATGAATGA
TTAATATCTTATGGTTGTGTGCAGATTGCATTGGGTCGGCATTTAATGTT
AAGGGAGCTATGCAATGTCCGAACTGTCGGAAAACTGAAAAAGGTCAATG
GCTTTATTCAAATGGTTCCCGTCCATATACCGAAATTAATATGGAGGACT
GGGTTCCTGACGAGGATCTTTATGATCACAGCCATTCAGAAATGGTAAGA
AAATCTTATAAGGCAATTTACATAATTATCGCTTTTGTAATTTTTTCTAG
AATCATATCTGAAGCGCTATTGCGCTTTCAGTCATTAATGTTAGAATTTA
GCTTTGTTTCTTCTTTCCAAGTAAACAATTAGTGCATTAAAGACCTTGTA
GACCACACACACATGTAAGAGGTTGATGTATAGTGTTGAAGATCATGTTT
GTATATACAGAAAGTTTGATTGAATACTTCTGTGGTGTGTGGGGTTTTTG
TATCCAGGAAATTTTCCTGCGTAATTTGATTGCGGCATTGGTCAATATAT
GCTCCAGTTACTGCTAGGACTAGTTTACTGAACTTTGTTGTTGTTGTTAT
AGTAGTTGTTATTATTATTATTATTATTATTATTATTATTATTATTATTA
TTATTATTATTATTATTATTATTATTATTATTATTATTATTATNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG
GGGGGATTGTACTTGCATATTTTAGATCGAAAAGGAAAATTTTGTTCTGA
TATGAAGGTCTAAATTCAATGTTTTAACCGAATTGTGATGGGGATATTTT
TGACGATTTTTTAGGCTTGCTGATGCAGAGAATTTAAAAAAGGAAAAAAA
AAAGATACGTAGGAAGAGATAGATATCGCTCTTGGTGACTAAATTTATTT
TCATTGGAGTGGACCACTTAGAAATATGTGAGCAACTGAAAGATTTGACG
TAGCTCAAATGAAAGATCGTTGACGTCTTTTAGATCAGTTGGGGAATGAA
TGGGGATTGGGTGTCCAATTAATAATTAATACTCCCTCCATACCAATTTA
GATGAGCCTTTTGCTCATTTCACACATATTAAGGAGTATTAAAGGGTTGT
TCCTTTTTCCATCTTTACCCATACTTATTGTGTTGACTTCTTTTGTATAT
TAGCTAGTGGTACATTGAAAATGATAAATAAGAGAGGGTAACAATAGAAG
ATTGTTGATAAATATGCATAGAAAAGTGAGAGGCTCAACTATTTTGGGAT
AAATTTTTTTCTCAAAAGGGTTTTAAGTACAGAAAAGAAACTATGGTCCT
ATAAGTAGGTATGACCTCAATATATGCCTTCCCATTTTTATCAAAATAAG
TCTGTCTATTTAGGCTCAACTATTACTTTAACTGTTTCTTTTTAGTTATT
TGTCGTCATCCCTAGACAAATGTTCCATGATTGCTTCAAGAACTTTTGTT
TGATTTTCTTGGCTGGTTTAGTAAACCTTAGAAGCGGGTAAGCTGTTAGC
TGCTGTTCGAAATCACTTTGTTTGCATTTGCTTGCTGTTCATGATCAATA
CTTAGCGGTCTATTGCTTGAACTATGATATGCTCTCTTACACATTGATGG
TTGCATCATTTTTACTGCTAACCTTTCGAGTGAACTCATTCCTGCAGCAA
GGCTGCTTTTTTCAAGTTTTTGACAGTTAATGGTTGCTTAGTGTTATTCT
TTCTTCTAGAACTACAAACAAAGTTTTTTTAACTTCCGAAATCATAATGG
CTAATATATTTTTTGTTGCTAATCTTTGCAGTCGTTTGGAGTTCACTGGT
GTCCCTTTAGTGGATTAACGCGACATCCATCATCCTTTGAGTAAGCACAC
ATTCCATCTGAAAATTTTCTATTTTTGCCTTGGAATGTTTTCATTTCATT
TTCGTATTTTAATTCTTAGAGCTGTGGGGGTTATTTTTTTCTTTTCCCCA
GTTTTTCTCTGAGTCCTTTCTATGAGCAACTTTATTTGTTTTTTGCATAT
TCCAAAAGCTGTCTATTTTGCTCTATTAGACTCTAGCCGATGGAAGTACA
TAAGTAATACCAATGAGCACTTGCACTTAGCTGACACAAGTAATAATTAA
TAGATACTAGTGTTTAAGTAACACTTAACTTGCATATATTGTAATATAAA
CCATGTAAATGTTTACCAGCACTCAGCATGCACAAAGCACAATCCCTCTG
TTGATACCGGTGTTTCAAAAAAAAAACCTTGTTTTACTAGTTACGACCCT
GAAATGATATGGATCCAAGTATGTCTATTATAATTTTAAAAAAAAAGTCT
GTCTATTATATGTAGCCTATATAAGGCCTGGGACAGGGAGTTGAGAGTTA
ATTTATCTGGATTCCAAGTTAAGTGTGAGAGGCTCTCTCACAGACGAGTC
TTGTTCAGACCAATACGATATAGACTCATCTAAACATTCTTTTGTGTCAA
GGCGTGTGACTAGATCCTACGTCAAGAAACATAACACTAGGATTTCTTCT
TTATATTTAGAATTGGAAAATATTCATTGTTCAAATCATATATATTTTTC
TGACATCGTGCTTTTATTATCTGCAGTGAAAGTGATCTCTCGCCAATTCC
ATGTAAGTTTAGTTTTTTGTGTAATTCATAGTACTCTGTGACCTTTAGCA
ATTATAGACCTCTGTTTTCTTTTTGTCAGATCATGACCTTCTTGGACAAC
ATGCTGTATTTGCTGAACATGCAGCTGTATCTTCTGGTTCTCATCATTGC
CCATATGTTGCCTACTTTGGACCTTTTCCCTCATCTTCAAGTTTCAGGGG
AAGTGTTTCTGATGGCTCTACTTTCAGCAGTCACTGGAACAGCCGATCAG
CTGCAAGTGAGATGCCCACCTCTTATGCTTTTCCCTCTGTGGATGTCCAC
TATCACAGTTGGGAACAGCAGTCATCTCTCTTCCCTACAGCAAGCAGCCG
CGTTCCTGGTCCTGATCAGGCCTCATTGCCATCAATGACCCAAAGGGCAG
CGAGGAACAATTTTGATAATCCAAGACCAGGATCTTTTGTCCATCCGTTT
GCTGTTGGCCATGGCCATGGGTAAGCTTAAACAACCTTATTATGTTATAT
CACTATCAGGTAGCTTGATTCCCATAATTGTTCTGTATCTTCTGTATGTG
AAACTGGAAAAGAAAATGCTTTGTGGATAGTGTTTTGACAAAAGCATATT
AGAATGCATCCAATCTGCGGGTCACTGGCATCCTATCTTTTCGTTACCGC
TCCGTGGGTTGTTTAGGACGAGCCAAATTTAAATCAAGTGCATGTTTTAT
CTCTTATGTGGGTTCATTGTTAGTTTTTATAAGCTTCATTCTGGCAATGT
AATTTTGAGTCATTGTGCTGATTAAGTGACCCACACAAACCAATAAACGG
GCAGTCATTTGTGGAGTATAAAATATAATTTTAAAAATAAATGATATTTT
TTGTAACTTCTTGTACATTATTAGCACGACTTCATTGAATGAATCTGTGT
AAAGTGTCGATACTAACATTTAGTATCATTGAAGAACTGTTGAATTATTC
CATTAGACATCCAAAGCATGTGCATCTCTTTCAATCTTTTTGTCCCTTTC
CATTTAGGATGTTAAGTTTTCATGTGATTAATAGTTCTAATGCTAGGTCT
GGGAGCTCGATTGCTGCCTCAATGTTTCCTCCATACCCTGGCAGTGTTGC
TCGTGCCAGGGAGCGGGCTCAAGCTCTTGAGGCTTATTTCCAGCATCCTC
CTGGCAATTCACAAGGCTTACATACACCGGTCATGCCCACCCTGCGAAGG
TCCAATGGTCACAGGAACATGGCTCAAGGTGATACACTTGCCTTGTCAAT
TGAGCACGGCAATGGCTTTTACTTCTTATCATCAAGCCCAACAGCAGGAA
GAAATTTTGCAGAAGCAGATAACTCGATGTCAAATCATTTCTATGCCTGG
GAAAGAGAACAGTTTCCTTCCTTTCCATCAAGTGAATCTGATAGAGATCC
TATATGGGGGCTCGTCCATCATCAGCTTCCAGGTGCCCCTGACACCGGCA
TCAGGCCTGCCAGCTTTCGTCAGAGGCATGGATCTGAAAGAATGACATCT
CAGCACCGGTCATAG

Sequence Length:

6615

Sequence Checksum:

ae3971cc56e40f30bbf3082b0cec9bd3

View location in JBrowse:

DCARv2_Chr6:16258657..16265271+

Cds:

>DCAR_022143cds ATGGCCACCGGAGATCTGGATCTCATGCATCCCCCTCCCCCTCCCCCTCC CGCCGACTCCGGCGCCGACGCCGGAAAAGAAGCGTGTTCGATTTGCCTGG ACGTTGTCTCCGATAACGCCGATCGATCCTTCGCCAAGCTTCATTGCGGC CATCTCTTTCATCTCGATTGCATTGGGTCGGCATTTAATGTTAAGGGAGC TATGCAATGTCCGAACTGTCGGAAAACTGAAAAAGGTCAATGGCTTTATT CAAATGGTTCCCGTCCATATACCGAAATTAATATGGAGGACTGGGTTCCT GACGAGGATCTTTATGATCACAGCCATTCAGAAATGTCGTTTGGAGTTCA CTGGTGTCCCTTTAGTGGATTAACGCGACATCCATCATCCTTTGATGAAA GTGATCTCTCGCCAATTCCATATCATGACCTTCTTGGACAACATGCTGTA TTTGCTGAACATGCAGCTGTATCTTCTGGTTCTCATCATTGCCCATATGT TGCCTACTTTGGACCTTTTCCCTCATCTTCAAGTTTCAGGGGAAGTGTTT CTGATGGCTCTACTTTCAGCAGTCACTGGAACAGCCGATCAGCTGCAAGT GAGATGCCCACCTCTTATGCTTTTCCCTCTGTGGATGTCCACTATCACAG TTGGGAACAGCAGTCATCTCTCTTCCCTACAGCAAGCAGCCGCGTTCCTG GTCCTGATCAGGCCTCATTGCCATCAATGACCCAAAGGGCAGCGAGGAAC AATTTTGATAATCCAAGACCAGGATCTTTTGTCCATCCGTTTGCTGTTGG CCATGGCCATGGGATGTTAAGTTTTCATGTGATTAATAGTTCTAATGCTA GGTCTGGGAGCTCGATTGCTGCCTCAATGTTTCCTCCATACCCTGGCAGT GTTGCTCGTGCCAGGGAGCGGGCTCAAGCTCTTGAGGCTTATTTCCAGCA TCCTCCTGGCAATTCACAAGGCTTACATACACCGGTCATGCCCACCCTGC GAAGGTCCAATGGTCACAGGAACATGGCTCAAGGTGATACACTTGCCTTG TCAATTGAGCACGGCAATGGCTTTTACTTCTTATCATCAAGCCCAACAGC AGGAAGAAATTTTGCAGAAGCAGATAACTCGATGTCAAATCATTTCTATG CCTGGGAAAGAGAACAGTTTCCTTCCTTTCCATCAAGTGAATCTGATAGA GATCCTATATGGGGGCTCGTCCATCATCAGCTTCCAGGTGCCCCTGACAC CGGCATCAGGCCTGCCAGCTTTCGTCAGAGGCATGGATCTGAAAGAATGA CATCTCAGCACCGGTCATAG

Pep:

>DCAR_022143pep MATGDLDLMHPPPPPPPADSGADAGKEACSICLDVVSDNADRSFAKLHCG HLFHLDCIGSAFNVKGAMQCPNCRKTEKGQWLYSNGSRPYTEINMEDWVP DEDLYDHSHSEMSFGVHWCPFSGLTRHPSSFDESDLSPIPYHDLLGQHAV FAEHAAVSSGSHHCPYVAYFGPFPSSSSFRGSVSDGSTFSSHWNSRSAAS EMPTSYAFPSVDVHYHSWEQQSSLFPTASSRVPGPDQASLPSMTQRAARN NFDNPRPGSFVHPFAVGHGHGMLSFHVINSSNARSGSSIAASMFPPYPGS VARARERAQALEAYFQHPPGNSQGLHTPVMPTLRRSNGHRNMAQGDTLAL SIEHGNGFYFLSSSPTAGRNFAEADNSMSNHFYAWEREQFPSFPSSESDR DPIWGLVHHQLPGAPDTGIRPASFRQRHGSERMTSQHRS*