LOC108226438

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108226438
Identifier: 
LOC108226438
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017401400.1, is a part of gene, LOC108226438.
The genetic_marker, MK004158 K1602, is located in gene, LOC108226438.
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
NCBI Daucus carota subsp. sativus Annotation Release 100

The RefSeq genome records for Daucus carota subsp. sativus were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.

View the full report at https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Daucus_carota_subsp._sativus/100/

Data from this analysis can be viewed in JBrowse here.
Transcripts: 
Transcript NameIdentifierTypeLocation
XM_017401400.1XM_017401400.1mRNADCARv2_Chr6:20890575..20898058
Sequence: 
ATCAAGATGGATTCATAATTGTTTCAATCAAGAAAATTTCATATCAGCTG
ACAGCTGTTACAGGTGTTCTGTCCGGGTTTGGTTAGTGGGCTTTTTTATG
GATCGGGCCTGTTTGCGGACAAGTGTACTATCAGCTATTACAGGTGTTCT
GTCCTGTCCACATTCATGTCGCATGATGATAACAGACTATTGAGCACAAG
GCAATAGGCAAAAGTTTTGTGCGCTACGCCTATATAGATTTGTTTGAAGC
GTTGTGCACTTGTTTTTCTGGGGGTTTAATTATTTCAGTTTGTGTTTGTA
AAAATGGCTGGAATGGCGAGTGGCACCAAAATAACGGATATGGGTATGGA
CTCTTTGATTCACTGCGCCAGCTTTCTCAATCTTCAAGATATCTCCAATT
TGTCTCTCACCTGCAAATACCTCAATTCACTTGCTTATTCTGATTCCATC
TGGCGATCCTTCTTCAGGTCTCTCTCTCTCTCTCTCTCCCTCCTCTCTCT
CTTTCTCTCCCTCCCTCCCTCTCCCCCCCCCTCTCCCTCTCTCTCCCTAT
TATAACTGTACGAAACAATGGGTCTCACTGTTCACAACACACCTATATGT
GTTTGGTCAAATTATTAGAATAATTTAAAGTCACGTGTTTATTTTCTGAA
ATATGTACTGATGATTGCAAATTGCGTTACTAATGTTTCAGACAGAGATG
GCCTCAACAAGAACCTTCTAGCATCTCAGAACGCTCAAGTGTGAGAGAAG
CATACATCACTAGAAATTTTGATGTGCAGCAATTTAAATTTGTTGACCCT
TTTGCTGCTGATATTCTCACTGATGCAAAACCTTTTGACAATTTGTTCAT
CAACAAAAATGATATTGTTTTCTCACAGGTGATATGTTTTCCACTATATT
CAACTCTTAATGGTTTTGTGATCTATTTTATTTAGAATTGGTTTTGCATT
GTATGGCATACATGTCACAAAGACGGCTTCACAGCTTTACTAAATTGCAC
AATCTTTTTCCATTTGGAATTCCTGTATTGTTAATGTGGAAAGAATCAAG
CAAATTGTTATTCAAGTCTTATTTTTTGTAGATATCTTGTTCGATACAGT
TAAAAAAGAAAGTCTCCACACAAATTACAGGAGATTGTAGTTTAAGAACA
TGGAAACTACACTTACAAGGACACAAGTTTCTATCAATAAATAGAGAAGC
TTGAATGAGAAACAAAAACTTTGAAATAATACGTGAACGTGGGGGTAATA
TCCTGATCAAGTTCCAGTTCTTGTCTGAATGCGTTCATTGTTATATAAAT
TGTATACTGTTTGTAGTACAAAGAATATAGGACGTGTGAAATCCTTTCCT
TAATTGAAAAATAAAGCTAATTTGTGTATCTCTGTTATTAGGGGTGAAAA
AATCAAACCCGACAACCCACATGAATTCGGCCTTTAAACCCGACAACCCA
CATGAATTCATTGTAATATTAATGAATTATCATATTTCGGTTGGGTTCTG
GGTTCTGGTTGATTATTCAGATCCATTAAAATTTCGGGCCCGGTTCCGGA
AATTGCCAGCCCTACCTGTTATAATTAAATATGTCATCCACCTGATACAA
TGGAAGTGATTTTTACTCTTTAGTTGAAGTCTATAAATGATTCTGCTCTG
TATTATTTGTGTGGCTGTCGGAGAAGGTGGTAGACCAATCCCACTGATCT
GGCCTTATGGGTTAATGAATAATGCATCATGGTCTTTATTTGTTTAAAGA
ATGATACTGTGATACTTGAATTCGATAAAGAAAAATTAATAACATGTCAT
GGAATTTCATAAAATTTATTAATATTCATTTTACATGCATAAGATCTTCT
TTTTTTTGCATATATTACCAATTAATACGTTCAAATGATACCCGTGAACA
GTCAGATTATAAAAAAAATGAACTTGAGGATTTATTGATTGCCTGTGAGT
AGTGACGAGGTCCCTCCCCTGATCAGAGTCATGGGACAAACCATCATCAT
CCCCAGTGTATATTTACTAAATATCTGAGTTTATTGATGTGATTGGATGA
TGTTTTTAGCTTTAGTTTAGGGTGCTAGAGATGTTATTGATTCGTCTCTG
CTTAGTGTCGTAGTAAGATCATGTGAAAACATATATTGACAAAGTATCAC
TATTATCTTTCACATTAGTACCAGAGAAATACTACATATAAGTAGTAAAT
AATTAATATTAGAATCACTGACATGCATTAAATTTGTCTTCTTTGGAAAA
ACGTTCAGGGTCCAGCAATAAACATAATGAAGATTGATAGCTTTCTAAAG
AGAAGAGAGCCTCTCCTAACGCTCCGTGATCATAGTGCTCGAGTCAGTTG
TATGAGGTGAGACTTTTTGTCATAAGACTTTCTTGTCGTAATATTTTACT
TCTAGTTTGATATGTCCAGATATACAGTATACTGAACCTCCTCTCTTTTC
CTCCCATGAGAATCAAACTTAAAAGTTCCAAAACTGAAAGTAGGACTCGC
GGGAAATCACAGCGACGTTTTTATTAAAAAAGAAAATATTGCAAAAGGAA
AGAATAAGAAAATTACTTGGCCAAATATAAAATTTAGATTGCGAAGGAGG
TAGCTTGTCAGTTGCCAAAATGGCTGGTAGAATGTTGCATGGAATTAAAG
AAAGTCTTTAAAAGTATCTTCTTGTTAACTTAAAAAACCGCCTTTAATAA
CTTTTCTCCCCTTAAATTGCTTTTTTAAATGCATGGGTCCTCTCTCTCTC
TGTGTGTGTGTGTGTGTGTGTGTGTGTCTTTTTTAAATTGCATGATTTTA
TTTTCTTGTAGGTTTCGTTCCAAGTTAAATATACTGAGTATATATATTTG
TTAATATTTTTGTAAAATGGTTTTAGGTTTTTACACATGTTCCTCGTAAT
TGATTTTATATTTTAACATGCAAGTGTGAACCTGATTTGTGATATGGTAC
GTCAATTTTATTGAAATTAACTCCAAGTATATGTATGTTTGCTATCGCCA
TTCGCCAGAAAAGCAAACTGAGATTAAAGATTTTGTTTCACAATTTTATG
TGTTGGGTACTGCTAAGATTGCAAAGAGCTTCTGTTAGAAGACATTATTG
TAATTAATAACTTGAGTTGTAAATTACAATTTTGTAAAATTCTGATGTGT
TTTGCAGATTCTATTCTCTCGATGAGACTTCTTTATTCCGTAGTGAGACA
CAAAGAAATGAGAAAGTTTTGGTAACATCAAGCTATGACCACTCCATTCG
CCTATGGTGGAAGGTATTGCGGAGTGAAGTTTATGTATATGATTGTTAGG
ACATTGAATCTAATGTTTCTCTTCTTCCACGCATGTGTAAACTTTACACT
ATGTATGCTGCATTTGCAATAAATTCAAAAAACGTTATGTATGCACGAAC
TTGTTCTTAAACATATCAAGATATGTGATAGATTATCAGCAAAATGAATC
TCTCATTAATGAACACAGGGAAATTGCCAGAGATGTTTCAGAGGTCACAG
CGGGCCAGTTACGACACTTTCAGATAAATTGTTGGGTGAAGGTAGTGGCA
AAGTATTTGCGAGTGGAGGTGATGATGGTACTGTTCGACTCTGGTCACTA
AACTTAAACGGAAAGCGTGGTCAACATGCTTTAAGAGCTACACTTTATGG
TCATGGGAAGCCATTAGTACTGATGTCAGTTGCAGGGTATGGACTTGTTT
CTTGACATTTATCTGTTCGTTCTTACCCTTGTCTATATATGTCTTGTATG
TTAATGCTTCAATTAGTTTGCTAAAATAAGTGCGACAAAGAATATAGGTG
TTTGCATTTTCGGAAGTCCACAGCCGGTATATGAAATGTGAAATTCTGTC
AAGGAAACATATCTAATTTAATTGAAAAAGAACTATAATTACTATATAAA
TTTGTTAACTTGTGTACAATATGCTTGTTTGCTGGAATTATCAAGTTTAT
TTTTTATTCAATAAGAGCTATGAAACAAATTAATTATTTCGTTTTCAAAA
TATACCTACCACTTTTAATTGCTTAGGATCAAGGATGTTGTACACAACAA
AAACTGAAAAACTGCTTTCTTCACATATAAAAGGTGTAGCCATGCAGAAA
GTTGTTCAAGGGTGCAGTATTCCACAACTTAATCATCGGTCTGCCACACT
AAAAGTTGGTATTGTTAACTTCTAGCTTACAACCAGTGCAAAGCACGAGC
GATCATAAATAAGTTAAATATATATTTTGAATATAAAATTTTATTTTAAT
TTAACAAGATTATATTGTTTTATCATCTTTTAAGTTTAACTTTGTTTTGA
TTTAAAAAAAAAAAAGTTTAACTTTGTTTTAAAAGTTACTCTAAACATAT
AATATTAATGAGATTCAATGTAAATAATGATTTTGAGCAGTGATGAAAGT
GAGTTTTGTAAGTATATTGTCCGTTATATGATATTAGATTGCAAGTATAA
TTCTAAGTATGAGTATGTAATATTTAGGATATTAATTCATAAAAAAAATT
TAAAAAAAAATTGTTAGCAAAATTTTTTTAGGTTAATGAAAACTGATTGA
TTGAATACAAAAACTTTCCAGTTTGTTATAATAGTATAGCAAGTATTTTG
TTCGTAATTGTATTTTGAAATTATATAATATTTAAAGGTTTCATACAATT
TTATATGGACAAATTTTTTAATTGAAATGTTAGTGAGATTCAGTTTAATG
TTGCATTTCAAAATATATATAGGTTGTTCTGAGTTTTAGCAGGGATGAAA
TTGAGAGTGTACGTATATCGTATTTGGTAGGACTGTGTTATTCAATTATA
AAGTTTAGGTGTATAGTTTAAATGTCATTAAAAAATAAAAAAAGTTAACC
AAAACTTGAATAACCAAGAGTTGGGGTTAACCAAGGTCGACTACAAAAGT
TTTTATGTTTGGTTATTATAGATAGCATACAGATATGAAGTAAATAGTTT
ATACTCCTCTATCCTGAAAACGGTGCTTCTATTTTCGCTCTTTAAACTTA
TGTTCCCACTTGTGCATAGGACTTACGTGGAAACAAATACAGTAGTGTAT
GTGATATTGGACTTGCTGATTTGGAACTAGCACAACAAAAAAATATTTTT
ATGATGTTATATATTTTAATTTAACCTAAATAAAGATAGACAGAGTAGCA
CCAAACGAAAGAGGTTGCTCAAAGAAAAGGGAAGAACATGTCCCTGAAGG
TAGCAGTATATCCCGTTTTGTGGGCATCAAAAGCTGTAGATAGATATTAC
TTCCATCCAACTTGTCATGTCCTAATTTGAATTTGTTGGTCATATTAACT
AAACTTTGACTACAAATTAAAAATTATCTTTTGATGTATTCATAAATCAA
AAAGTTGAATCTTAGAATCTACTGAACATTGTTTCCATGATTTCTTTTTC
CAAATTTATATTTTTGTCATATAATTTAAGTAAAATACATTATACAAGTT
ATTAATTCAACCAGAATTTGGTCAGAGCGTCAAAATAAATGAGATGAAAG
GAGCACCGTACAGTTGCTAAAATGATTTTTGTAAGATCCGACTATAGCAT
AACTAATTTTTGTGTCTTGCTAACCAGATATGTTGACAACATTTTGTTTT
AGCCCTAATTAAACATTCTGTTTAACAACTTCATAAATTTGAACTTGTGA
TTGAATTGCATGCATGCTACCTTTTTTTGTTTCCAGGCACAAAAGTTCTC
TTTTGGTGAGCATGTCCAAAGATTCAAAGGTATTGTCATCCTTGTAAGAT
TAATTTGTAACTTGCAGGTATTTATTCAGTTTTAGTCAAAGAAATGTACC
AACTGGATAGATATTTCTAATTAAATGAATCCATGTGTGTTCATAATTTA
CATAAGCATAAATTGATGGCATGTCACCGCTAGTAGTGGATCTTCTCTAA
AGTCACTTTACTTTCAGATATAGTTTTGAGGCAACAAGTTTACACTGGAC
CTACAAATGCAGTGAATAGGATATATTGTTAAAGATGAAAACTGTGACTA
TATTTCTGACTGCATAATTTGTAATTTGTAAGCATAACATTTTGTAGGTT
TGTCTCTATTATATTTTTTGTGATTTTCCTACGTAAGAATTGCTATTATT
TGAGTTTTGATGTATGATGGGGAATAGTGTAATATTTTTATATTAGTATG
TAGCTTACCTAGTTCACTTCTTGATTTTTTAGTAAGCGTCATCTGACAAT
TTTTATCGAAATTAGTTGAGGCTTTGGGATACCGCTACATCATCTTCGAG
TTCTTCGTGCTGTGTCGGGATGACTTCGATACCTGGTGCACCTGTTGGCC
TGAAATGCCATGAATCACTTCTTTTTGTAGCTGCTGGTTCTTCGGTTGTT
GCAATTGATTTGAGAACCATGAAAAAGGTTTTCAGCACACCATATTATCC
GCCAAGTTTGTTTTCATTTGAAATACTTCCTTCCAAATCATTAATCTGCA
CTGGTGGCATGAACAGGTACACACTAAATTTCAAGTTTTGTTATTTTGAA
GAATACTGAATTATATGGAATCTCTTACAAAGTTTTTCTCCTTACCTTGG
TTGATTTTTTAGCATCAGTCACCTTTCTGCAGTTAATTTGGTGTTGAGAA
ATCTTTGCAATCTCAATCAAGTTTTACCCATATTAAAGGCATTTTCAGTG
TCATAACTAAAATAATTCATCTTCCATTCTGCCTTCTTATAGGACTTGTA
TAAATATTTGGATTTCTTTATTTCAAACTGGAGTTGCTGAACTAGTTGTA
TTTCCACAACTTCTTCGTTTGTGTTGGGCGTTTTATTGCACCCATCTGAA
ATCACCTTTGTAGAATGTAGTATATTCAAAAGAAAATTAGGTCTATCCAG
ATCCGTGTTGTAGCAAACTTATCTTGATAGATCGTGTGTTAGTGTTGGCA
GTAGCTTTTCGTTAAGCTTTTCAATATGATTGTGTAGTCTGTAACAGAAA
TTTTCAATATACTCCACAGTGCAATGCTTTGGGATATGAGAACATTCTCT
GAGACGGTGAAAACAAAGCCTTTAGGTTTGCTGGATGGGCATATTGGTCC
AGTCAAGTTTTTGCACATGGATCGGTATAAAGTAGTTTCAGGAAGTCCTG
AGGATCCATTTGTCAATGTTTGGGAGTCTGACACAGGTCGACAAACAAAT
ATCTTGGCTTGCAACCCTACTGGTGGTCTGCATTCTACCACAGGTGGTTC
TGCCATTGCTGTTAATGGTTGTGAAATAGTCACTGGTAGCTGCACTGAAG
GACAGGGGATTATACACTACAGGAACTTCAACTATGCTACCAGTCAAGTT
TTAGCAGAAGAGAATGAAGGTGGTTCGAAGTTTTGGGGTCCTCAACATTG
TAGTGACAGTTATGAATCTGATAGCTGATCATGTTTCTTGTACCAGATAT
ATATTACAAGCAGCACAATGTCTTGTGAATTTTGTTTGTGAAAAATAACA
GTAGTCGTTATAAGTTTAAGTATTAATATCTCA
Sequence Length: 
7483
Sequence Checksum: 
6ffe9d1414c693231918e3fe6319c4ee
View location in JBrowse: 
DCARv2_Chr6:20890576..20898058-
Gene: 
LOC108226438
Gene Biotype: 
protein_coding
Gbkey: 
Gene