LOC108219775

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108219775
Identifier: 
LOC108219775
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017393284.1, is a part of gene, LOC108219775.
The genetic_marker, MK004104 K1548, is located in gene, LOC108219775.
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_017393284.1XM_017393284.1mRNADCARv2_Chr5:34436175..34443415
Sequence: 
AGCGATCGATAATACCAAGAATCCAACACCCGCTTTCTCTCTCCTCATCA
TCGTCAACACTCTTGTTCTCTCCCAATCTCTCTCTCTCTCCCGCACACAC
AAATATCTACATACTAATGGGCTTGAAAGATAAAAAATCGAAGCAAACGA
ACAGCAGCAATCAGCAGCAGCACCAGAACGGTGGTCACTTTTCTCCTTTC
AAATTTGCTAAATTGGTTGATCCCGATGCCTCCTGGGACAAGGTCTCTTG
CTCTTTCACTTCTCTTATCCTTTTAATTTGCTCTTCTTTGTGTAATTTAC
TGTCATTATATGCGTCTGCTGCTTTCGAAAATCTACTAATTATGGTTACT
TAGGCTTTCATTCTCTGATGTGCTTTTTTGATAGGGTTTATAAAGATAGA
TTAGGTGATTTGGAGTGTATTGGAAGTATTGTAGGCAGAATTATACGAGT
TTTGCTTCGTATAAGACGGTTTTTGGCCTTATAAGAGTTAGTTGGAGGTG
GTGACTATATCACATCCAATTGTAAAGAATTTAAAAGGAGGATGATAATG
TGATCGAGTGTTGTGAAGAGATTGATTGATCTGCAAAGAGGCTTTTTATA
AGGAAAATTAGACAATGTTTATCTTATTTTTGTGAGATCTGCCTTTTTGC
TTGGTCTATAATTCGACTTAGGATCTTTGATCATACATTAGTAACCACAA
CTGTTGATAGTTTCTTTGTATGCGTTTCATGCATCTTTCTGCCTGACAAA
TCTGGTGAATGAGGCTGGGGATTTGAAGCTGGTAGTGGTGTAGTGTATCG
TTTATACTCAGATGCAATTTTTATTCAAGCCATTGTATGTTTAGCCTTAT
TAGTTACTAGCTTGACGAAGGGACTCTTCAGTTGGGCTACCGTATGCGAG
TCTGACTTGCCCGGCTCGGCTGAGTGCGTATCAGACTCGCCAGGAGGCGA
GTCGGCATGAAAACAGCATCTGACTCAGCCCCGACACAGGATGACACATA
TCTGACTTGGACCAACTAGAAAAAGGACAGACCAACTAGATAAAGCACAA
CCATTATCCTTTTAACCTAATTTTCAAGCATCCGCCTATGTAGATGCACA
CATCTGCTATATATATACCATCAGAAACCCTATTTCAATCTCATTCTGTA
ACATCTATACTCTTGTTGAACCAGAAATGGAGTGTTTCCTTTTTACACAA
GATGGACAGAATGTTGACTGTTCTTTTATTAGTTTTCCACTTCTTTCGAA
GAATGAAACTTTTAATACTTGTTGTGAACTTATGATTTATGAAATAAAAT
GTGTAGTGTTTTACATATACAAATCTTATCATGAATATATATATATAAGT
AAATAAGTAAATGTGTTATTTGTATTTGCCGAGTTCTGTATCCAAGACTC
CTCGATGTTTGGAGAATCTCTGCCGTATCTGAGACCGTGCTTCCTAGGTT
AGTAGTGATTGTTATTTGATTTTCTGTTTTTAAGTCATAATAGTTTTTGG
AGTGAGGCTTTTTCTTTCATCCACTGAAATGGATAGAGGAACAGGACAAC
AGGTATCAAATTACTATAAGAATTAGTTATTTGAACTTCACATGAAAGTT
GAGACTGATATTGCGGCGTAGACTTTGTCTTTATAAGTGCAGAAATTGAA
TTCAATTACTAATATACTTGGAATTGTAATTCAATGATTTTAGCAATTAA
TTTTGGACATTAATTAATGTCAAATGCAAGCGCTGTTGTCATGATGCTGC
TTTTTTCCCCTTTGGTATGGGCAGGATTGCGCTTTGAATTTTTTTGACTG
CTGATGTTACACTTTTATTTTGTAGGATCAATTGGGCGACGTCCTACATT
GGATCAGACAAATAGTTGCCCTTTTATGCGGGTTGATATGGGGTGCAATT
CCTTTGATAGGTGGCATCTGGATTGTCATGTAAGTTGAGGCTTGTAAACT
TCTGTATGATGTAGTGCTGATAAATAGTTGTATGTGCAGTTCTTCAAACT
GAACTTGTCTGATATTATTGTTTGTTGCCTCACACTTTCCAAGATCATTG
ACAAAATTTTATGAACTTTAGTTTATACTTGGTGTTAAATTAAAGCAATG
TTTTTTTTATTTTATAAAAAAACTGCAGTAAGGAAATTTCTGAGAGTAAA
ATTTAAGAAGAAGCTGAGCATTGATTGTTTACTTTATAGCACCGATTTTC
TATTTCTTATATATAAGTCTCTTGCCTACTTTGTAATATGCAGCACATAG
ATTATATAAATTTAATATACACTTCCAGTTTCTTCTTGCCACGCTTCAAC
GGGAGGGTGCTTGTGGGCTTTTCCAAACTGGTTTTTTCTCCCGCTTCTTT
AAGACATAGTTAGTTGCCTCATTCAGCAAGCCGATTTTACCCCTTTGGTC
TCTCTTCAGTTTAGTGAATTTGCTTTCTTTTTTTCGAGCCTAGCACTGAC
ATGTTAATTGATAGTGTTTCTTAAGTGGAGTTTTGCTAGGGTTTCCTTGC
GTAGGCACACCACTGATTTGATTGTTTGTGCTAATTTTATTTGATGTTTC
TTGTGTCAACCATCTACGTATATAGGCCGAGGATTTTGGAAATAATAGGG
ACAGACTGGGTCGTATATATATGCGGATATTAGGTACATTTGTTACTTGT
TTGGGCTGATTTTAACATGAAGAAGTCAGACCCTTCCAATCGTAAGTTAG
AGCATCATAAACATCAGCCCTTGAGAGGTTGGTAAATTATAAGGTTTCCC
TATATATGCTCCAAACAATTAGTTTTTATGAATATCTTCCTGCTTCTAAA
TTTAGCGGAAATTACTGAAAGTACTTGTCAAGGGCCTAATGATTTCATAG
ATGATCTTAAGGGAATCCTCTACAAAATTCTCATGTTTTTAATGTCAAGA
TAAACCAATTTTCAAGACGAGGTCTCATTTTAAATGTCTACTATAGTACT
GACAGCAACACCTCTTGACAATAGTTTCAATGTCTGGTATAGTGCTGACA
GCAGCCAGCAGCACCAATTACAGACATATGTTTAAGTACATCATGTGGTC
ATGAGTTTGAGTTGGGTATCCCTGACGTCATCATAATTTCAGTGTCAAGA
TGGATCGATTCTTAAGCGGGGTCTTTTTGGAAAATTTAAGCTATGCTCAA
GGGCTTTTAGCGGTCCACTTTTTAATCCACGGATAGGCCTTTTAATCGCT
AGACAGGTAATAGAGTTAAGGCGTGTTTAAAGAACCGCGTTGTATAGCAA
TAGGGCTTGGGAAGAGGAGAAACAATTGTATATGTAATAAATTTTTGTGC
CCACTCTTCCCTTGCTCTATTCATGTGTATATATATATATATATATATAT
ATATATATATATATATATATATATATATATATTTACGCTTTATCCTAAAA
TATTGAGAGTTAGTAACATGATTGAGAATGACCTTTGTGAATACCAAGTG
AGTGAAGCTATGGACGAACATCTATATAATTACATGAAACGAAGTTGTTA
ATTAAATAAAGTGAACTCTAATCTCTTTAATTATAAACTTCTTTCTTATT
TCTCTTATGTTTTTCTGCATCGTGTTCATTTAATCCAAAAAATATTCATG
TTATTATTCCAATGTAACAATAATTGAAAAATTACAATCATTGTCATGTG
CATATAGATAAATTATCCCTTTTTTGCATATATTGATAGCGTGCAAAGTA
GCCACATTATCTATGGTTGTAAATATAGTCTTCTCAATGTGTACCACCAT
GCTATTGTTCACCCACTTATCCCCCATCCTATTAAGAAAATAAGATCGAC
TTGACTAAGCAATGACCCTTTAACATTTCATGTTGCAATAGGTTAACATT
TCATGCCGTAGTCGGTATAGCTAAATTTAGCTTGACGATTAGTTTTATGT
GTCTTTGTGATAACCATCTTAATATCAAGCTCTCCAATATCTTGAAGTAT
CCTGAGGTTAGGAAATTATTTCATCACTCCTAACATGATATTTTAAAATG
TTTAAAAGAACCAAGAACTCTCGAGTCTCAGTCCATAAGAGAAGATCTTC
TATATGTAATGGGGAAAACCAAAATAGGTAAACATATTTAAAACTTACAA
AACGAATTTTCGGGATTAGGAGAACAAATGCAAAAAAGTAAAATTGTGTT
CCCTTTTTGGAAGCAATTTCTCATCTCCTAAAAGATGAGATCAATAACCT
AAAAAGAGAATTTTAAACAAAGAGATATTAATGATTGTTAAACAACCATC
TCTTTGAAAATCTTTAGGCTACAGTTGAGGTTACAAAATGGATCCTATAT
ATTAACATTATTGTATGTTAATATAGCTTGTATGTATTATATGTTATTAG
TTAGAAGTAAACTTTATTGTACTTTATTGCAAAGTAAAATTGTATTGCAT
ATATAGTTTATTAGTAATATTCTAAATTATGGTAGAGGATAAGAAAAGAT
CTGTTTTCTTTATTATCAAGATTTTGCTTAGCGGCTAAGCTTATGGATTC
ATACTATATAAGGAGATGTTATATGTTATTATGGTAGATTTTGATCGATT
ATTGAAATTGAGAATTGATTCTCTCTTGTTATGGATTGGATCCTAACAAT
TTCTTCTATCATGCAGTTGGATTAGGTGGATTTTCTTGCGGTTGATCCAC
ATATATATCTTTTTATATTTTTAATCCCTGTCCAGCATTAAGTAGACAGC
ACCAAAATGATAGATTAATTCAAATAATGGGGTGGGACTTGTCACTTGGG
AGGGATCAAAGCCGAGACGTCTGCCCATATCTGAACCTGATGCCATTTTA
TGTGACTTTTTTCCACTATAACCTGAATGTGCTAGTAAAAGGTTCTAACT
GGATCATATACAATTAACAGTTCATGTTAGAGTTAATTTCATGACAATGT
ATTTATTCTAATATATTATAATGTATGTTAAAAATAGCTGTTAATGTGTC
GGGTTACATTGCAGAGGCTAGATACCAACTCTTTCATCCATGCTACCACA
TCTTGTAGTATCTATAGACTACTGATACTGATAGGCGATAGCAATGTTTT
TAATTTTGAAGTTTATATATCATTTATCATGCCTTGTTCATCGATTTTTC
TAGATAGTTGATCAATCTCATCTTTAAGACAACTGCGCGAGTAGGAAAAT
TATTATACATGAAAAACCCTATGACGTTTGCACCCTTTAATGCTTTTCAT
TCTAGTAAAGCTTGAGGGGAAGATGTTGTAAATGAGATATCATAAATTTC
GAATGTGTTTGTCGAAGAATAATCCAACTCAAACCTATCTTGAATGTATA
GTTATCTTGGGAAATGAACATGCAACTGACAAACTAAATAATCTGAACTC
AAATTAAATATCAATAAATATCCGTATATTATTATCGATAATGTATTCGA
GTACACACGTCATATGTGGGAAATACGATTGTTCTTAAAAAAAAAACATC
CATGATGCATCCTTAAATCCACAAAAAAGGTCATTTGATTTTTTTAGGGA
AATTATTCAACTTCTTCTAACTTTTGGTGCGCTCGTTCGGGTGAATGTAC
TAGAAAAAGGGAAGAATAAATTAATTGAAGTTGTTTTATCTTGTGGGTAA
ATGTTTATAAATTCAATTCCTTCATTCTGTGGCTAGCATCTAAACTAGAG
GCTCAACCTAGTAATTTGAGAAAGAATGATCCTTCCTCAATCTTACTCGT
CTCATCTACCTCCATTGTTTCTTCTTTATATATATATTTTACACTTTTCA
TTCCATTTTGTACTCCCCAATCAACGGATTTATAATAGGTTAAAATTTGA
CTTGCGTTATTATAAAATAACTAGGTTGTTTTTAAAAATTATATTTTTGA
ATGTTGCAAATATATTAAAATGGAACTGGCATCCAAACTTTACACTTGGA
CATTAGAACTATAGTTTTATATAATATTTACTGAGATTATAATAGTATAT
GATTTGCTTAATTACTTTGAAAGAGTTTGATTTCATGATTATACCATTAA
TCTATTGATTTCTTCATCGTGGCATTAGAAACAGTCAAAATTTGAGTTTA
GTTGCATGTTCATCAAATATGCTACCTATCGCTTGAGACACGCCTTGGGT
GATGGGTCTACTTCTTCAGGCATTTAAACCCCTTTTCCATGTTTGTCCTC
TTTTCGGTGTTAAATTATTATGCCTCTAAACAAGGAATTATATGAGAGGT
CTAGGGCCAATCAAGAATTTGGTTATATAAGCTTCATTGTCCGAAGTTGT
TGGTTGTTCAGATCTAATCTCATTCCCAACAATTTACCTCCGGCATAAAG
TAATGGATGTTGGCAATCGTGTGTCTGCTACCTGGATTGCGTTAATTATT
ATTATCTTGTGTATTTAATTTTCCAGTATAAATTGTGTTTTCAACGAGGT
GGATAGTTTGACACTTTTTATTCGTATGCTCATCAATCTTTTATGTTGCA
AGTACAATGCATAATTAATTTTTATATTGATGAAATAGTTAAGGCTTTTA
TGGAAATCGCTTGAACTTCTTTACTAGTAAGTGCAGATGGTAATTTGTGG
TTGCTGATTTTTGTTACAGATTTCTAGTTATCTCCTCTGCACTAATTTAT
GGTTATTATGCAATGCTGCTAAAAGTTGATGAAGAAGATTTTGGTGGTCA
TGGTGCTCTCCTGCAAGAGGGGCTCTTTGCTTCTATAACGCTTTTTTTGG
TAGCCTAAACTTCTGATTTTCTGTATGCCACTATGCTTGCTAGCAAATTT
ACCTGTTCAATAATCATAATTTTTTTTTTTTTTCAGCTTGCATGGACTTT
GGTTTACAGTCTGGGACACTTTTAATGGCCTCAATCTCATCAATACTGCA
GCCTCTCTTTTTCCTACCTGTAGCTTTCTATGAGTTGGCCAATTTTAGGA
CTCAAGCACATTGCTCCAGATAAGACCAGGAAATCCTGCAGTCCAAATCA
TTGAGCATTTTGGAACCATTTCTTCAGTCTGTGCAGTGTCAGCTTTCAGT
GGGCTGGCATGCTTAGCTTTTAATGATATTTAGTTTTTTTTTGTACTCTA
ATAGTTTCATTGGCGGGAACTCAATCATGTTTTAGTCAAGTAATATTGTG
TATGTTGTATTGATTTAAATGCATTATAATTCCATATGTACTTGTGGGAG
AAGGTACCTTGTGGTAGGTTTTTATTCTCAATTTAACCATCTCTATAGCA
TACCTTACCCAAATAAAAGAGGTGACATTTTTTGCAACAA
Sequence Length: 
7240
Sequence Checksum: 
7bab7380e759f366a430a4cf963ebc30
View location in JBrowse: 
DCARv2_Chr5:34436176..34443415-
Gene: 
LOC108219775
Gene Biotype: 
protein_coding
Gbkey: 
Gene