LOC108218800

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108218800
Identifier: 
LOC108218800
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017391920.1, is a part of gene, LOC108218800.
The genetic_marker, MK009563 4_21399312, is located in gene, LOC108218800.
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_017391920.1XM_017391920.1mRNADCARv2_Chr4:21393133..21400926
Sequence: 
AGCATAAAACAAACATATAAGTACATCTTTGTGAATATTATAAACTCAAG
CAAAGACAGTTTCAGTTCAATAGGAATCTGTAATTCATTGATTTTACAGA
TAAATTTTAGAAAAAGGAACATTCCTGGATGAAAAAAATGGAGTAAAGAA
ATGGTTAGGCAGAGGGTCACCCCACATACAAGTGGAGCAGAGAAAAGTAT
GCGACATGTAATGGGATTTCTCGACTACAGATTATGATTATCATTATTGT
CGTTTCTGTGCAAATGTACTCTATATATATCCAGTCAACAATGGTACCTG
TTCTTTAAATTTAGGTGGAGAAATAAAGAAGCATACTATAACCACTCTGG
AACTGAACCTGCACAGAGTTGTTTCAAAATGTGGAGGCTAAACATAGCGG
AGGGAGGTTCTGGTAAGGATCCATACTTGTACAGTACAAATGACTTTGTT
GGGAGGCAAACTTGGACGTTTGACCCGGAGTATGGAACCCCGGAAGAAAG
AGCCGAGGTTGAAGAGGCTCGAATCAATTTCTGGGATAATAGGTATCAAG
TTAAGCCTAGCAGCGATCTCCTTTGGCGAATGCAGGTTCTATTCTTTTTT
TTTTTTTGCTAATTGATTACACACGCACACGTGGGGAGTCGAACTCCCGA
CCTCCCGCAAGGGGGTACAGGAGCTCTACCGCCACACCAACACTTTGTTG
GCAATGCAGGTTCTATTCTTCTTCTCCACTTTGTGTTCTGCATCATATGC
ATAAATTATTGTCATACACGATCCACTGATAACACCTATGTGTATTCAAC
AAAAACTCTAAAGTGCTACTGTAGATATTAAACACATCATTATATTCGTT
CAACTACCTCGTTCTCTCAAAAAGTAGACAGAAAGAAATCCCACCACTAA
TGAGCAATGGGCCACAGGCTCACAGCTATCTGTTAAATGAGCCATGCTTG
AAAACAGCAATGCAGTATCTCACATTTTACTAAAGATTCTGAAGAAGAAT
AGTTAATTTTGCACTGGTCATCTGCTAGTGATATTATATCATTAAAAGCA
TTGCAATCATCTTCTAGATAACACCACATAGCAGGGCATTCTTGGGATAT
CACAGATTCAAGCCTTGTGGCTAAATATCCATTGGCAAACTTTCAGTGCC
TTGGATAAAACAGAGAGTGACAATTAAAGCATCTGAAATTGTATAGTACC
TAATCTGTTGAAATTACTAGTGATAAACTGGTGAAATATTATTCACAGTA
ACTTTTTCTTGATATGGTACCTTATTTTAGGTGGCTTAAGTGAATATAAA
TATATAATACTGCTGATAGATGTCTCATGAATAACAATTTTTAATTAATC
ACATACATTTAAAAGAACCCAGAGGTTTGCACAAATAATCTTTTCAAGTA
ATCACTTCATATGTATAACTGGGTCCACATTACTTCCCGTTATGTTGCAT
AATTACATATATATAAAGCTTATATGAAATATTTAATGATTCTAGTTTCT
GAAAGAGAAGAATTTCGAACAAACCATACCTCAAATAAAGGTTGCAAATG
AGGAAGAAATCACCTACGAGACGGCCACGACAACATTACGACGAGCTGTC
CGCTTTTTTGCAGCCTTGCAGGCCAGTGATGGTCATTGGCCTGCAGAAAA
TGCTGGCCCATTATTTTTCCTTCCACCATTGGTAACTCACTCCTCCCCGT
TTCATTTCTTGGTATACTTGTGCTGCTCCGAATTTCATCCTCACTGCAAA
AAAGGGGAAAGTAAAAGGAACAAATACATTCAATCAACTTCTTGTGCTAA
ATGATTATTATTACTGCTTGTTGTAAAACAAATATTGCAGGTTATGTGCT
TGTATATTACAGGACATTTGAATACTGTATTTCCTGCAGCACATCGGAAA
GAAATCCTGCGTTACCTTTATTGTCATCAGGTACATTTCTCGGCCCAATA
ATTGGTATTCCTAACAAAATGAGATCATTAGCATTTTTAATAAGTGACAA
ATCCCTTCATGATGGAGTGGAGTCAATTATGATATGGTCATCCGAAACAT
GTATATGTTTATAATTTAAAAAATATATAAATTAATTCATCAAATTGAGG
CAACAAAAAGTTTTGCTGATATATAGCAATTTCAGAATGAGGATGGTGGC
TGGGGATTACATATTGAGGGCCACAGCACAATGTTCTGTACAGTCCTGAG
CTACATCTGCATGCGTATTCTTGGAGAAGGACCTGATGGCGGTTTAAAGA
ATGCATGTGCCAGGGCAAGAAAGTGGATCCTTGATCATGGTAGCGGGATA
GCAATACCATCCTGGGGCAAGACTTGGCTCTCGGTAAGATTATTCTAGGA
CTTGCTTGGTAAAACTCTTGAACTCAATATATTTCAAGAAATAAAATGCA
TACAACATACTCAACAAATCCATATCAAGTTGATGCATATTTATATATTT
ATTTGCTTCATATGTAGATGCATTAAAGAACTGAATCAGATATTATAAGT
TTTTTTGCTTTCCCTAAGCTCAAACCTGTATCTTAAACCTTCATTGTTAC
TGAACTTGAAATTCCAGATACTTGGCGTATTTGAATGGTCAGGAACCAAT
CCAATGCCTCCAGAATTTTGGATCCTTCCTTCATTCCTTCCCATGCATCC
AGGTTCACTCAGTTCTATGTCAATACTCGTTTATATTTTGGATGCACGTA
GATGACCTTTTATCTTTGTAAATGAACTACTCTTCTGGTTTGTTTAATAT
CTAAATGATTCTCTCTTTCCCGGAAATGCAGCAAAAATGTGGTGCTACTG
TCGGATGGTTTACATGCCTATGTCTTATTTATATGGGAAGAGGTTTGTTG
GTCCCATCACTCCTCTCATCTTACAACTGAGGGAAGAACTATATGCACAA
CCTTATGACACCATTAACTGGAGAAAAGCACGACATAATTGTGCAAAGGT
ATTGCTAATGCAATAATGTTACACATACCGACATTTTTCTAGAAGTTAGT
GAGAACTATGGAAACATATAAAACCTAATAGAGAAATATGATTACAAACT
TCTATATCACGAGTGCGCAAAACAAATCCTTAAAGAAAACCTTACTATAA
CATTGTAACTAGACTCCTAGAGTCCCAAGCTAGTTGTAATATATAGAACT
CTCTGTGTCTATTTGTAATACATAATTATTTATCTCATATACCAACTTGT
TATCACAGGAAGACCTGTATTATCCTCATCCAATGATACAAGATTTGATG
TGGGACAGCCTCTACATATTCACAGAGCCTTTCCTGACTCGTTGGCCCTT
TAACAAATTAAGAGAAAAAGCTCTTCAAACAACTATGAAGCATATACATT
ACGAAGATGAAAATAGTAGATACATTACAATTGGGTGCGTGGAAAAGGTA
ACATGTTACATGATCTAAGGCATATAACACATATCATTGAGCATTGGAAA
GAAGTTTCTGACAATACCTTCTCTTTATCAAGTTAGTAGTTCACTTCTGA
CATCTAGCACTTAAATTGCACGAAATTCGAACAGGTACTATGTATGCTTG
CTTGTTGGGTTGAGGATCCTAATGGAGATTACTTTAAAAAGCACCTTGCA
AGGATCCCAGATTACATATGGGTAGCTGAAGATGGAATGAAAATGCAGGT
TAGAATAAATGTCGACATAAATTGTAGTAATAAATATCTTGAATATAAAA
AATCTTAACACTATGCATGAAACTCAATAAAGATATAATAAAGACACACT
TAACCCCCTAACTAGAGTTTCCAACACCAAGTAATCAAAAGGTTAAGCTA
TTTACAAATGTCGATGTAATTCACATAATCTCATATACTTATACATATAG
ATTGTGCACACAAAGTAATATGCCTAATCAAGATGCATATATAAGCAAAA
TGCTGGAAGCAAACAACTTCATTTACTTACAAATTACAATCCTTTTTACC
TGAGTCATAAAGACATGCAAATGGACTTTTATTGCAGAGCTTTGGTAGTC
AGGAATGGGATACTGGTTTTGCCATACAAGCATTATTGGCAAGTGATCTC
ACAGACGAAATTCATCAGACTCTTTTCAAAGGACATGATTTCATAAAGAA
ATCCCAGGTTCCAGCTTAAATTTACAAACTCTTCTTTATTTATCCTAACA
AGTCTACTCACCAGTAAAGACTGTTTATTAATTCTACTAATATATAATTG
CAGGTCACGGAGAATCCTTCTGGTGAATTTAAAGCCATGCACCGCCATAT
TTCTAAAGGATCCTGGACCTTTTCAGATCAAGATCATGGATGGCAAGTTT
CTGATTGTACAGCAGAAGGATTGAAGGTACTTATTCATATGAATCATCAT
ACTTCTAAACATTATAAACAAAACAGCAAAGATGAATCACAATGTCTATA
CTCTTCTGGTGCTTCAGTGTTGCCTACTTTTATCAAAAATGCCAACGGCT
ATTGTGGGCAGTAAACTGGAAGACAGCAGATTGTTTGATGCTGTCAATGT
ACTGCTTTCCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNAATCTCTTTCCCTATTGTAAATGTCATCATACTA
TAGGTAATTAGTCTAAGTTCTAAAGAAAGCTACAAATGTTGTACATGATT
AAAATGCTACTCTTTTCCATTGATATAAGATCATGACTATTCATTTCCAT
CCGTAACTGTAGAGTAAGAATGGAGGACTAGCTGCATGGGAACCTGCTGG
GTCCTCAGAATGGTTGGAGGTAGTTTATTATACTTGTTAATATTATAGTA
AATATTCATTCACTCTAATCAAAGTGAGAGTCCATGAAAGATCAAACCTG
AAACACTATTAGAAACACACAACCACCGAAGCAGAAAAAAAAAAGATGCG
GACGCATGAAAATCCTGAACTGAGAAAAGCACAGGAGGAAGCTAAAACTA
CAGTCAGGATGTCTAAAATGATAGATGCTGAAAACTAAATTTATTCTTTC
CTGTGAATGGAGCATACCCAAACTGGATCCTCCAAACAAGAATCCAATTT
TAATAAGTTTTTCTTGATTGTTATTTAAAATTACTCAAATCATATGTTTC
AGCTGTTTTACAGCAAAAGACTACGAACCTGGAAGACAATTAGGCTACAC
TAGAAGATAAGCCTAACAATATTTAAAAAGTCCTTGAGTCAGCCTTTGGT
CAGAGTGGCCTCCCCTCCAACAGCAATGCTAAACCAAGCTTACATGCAAA
AATAGGCTCAGAACTATTAGAATCTTATACGTCCTCTTTCACGCAAATTT
ATATTTCCGCACGTATTGAAACTTGAACAGAACATATGCAATGTATAGAT
ACTTAATATGTTTATTGAACTGTTTGATCCTGCAGCTGCTTAATCCTACA
GAATTCTTTGCAGACATTGTCATTGAACACGAGTAGGTTTCATTACAATT
TTTAATTTTAAATGACGTGTATACACTATTGAGCATAAGACTAATGATTA
TAGATTCAGGTATGTTGAATGCACTTCATCTGCAATACAAGCAATGGTTA
TGTTCAAGAAGTCATACCCTGGGCATAGGAAGAAAGAGATAGAAGGTGCT
ATCTTAAATGCTGTTCAATACCTTGAAGACATACAAATGCCAGATGGTTC
ATGGTATGTTCCATAGGAGAAGTGATATAATATTTATACTTGAAACTTGC
AAATTCTAAGCATAGGGCTGACTAATACAGGTATGGAAATTGGGGTGTGT
GCTTCACATATGGCACTTGGTTTGCTATTGGTGGTCTAACTGCAGCTGGA
AAGACATATAATAATTGTGAAACCATCCGCAAAGCTGTTGATTTTCTTCT
AAAATCACAACGCAGTGATGGTGGTTGGGGAGAAAGCTATCTTTCTTGCC
CAAACAAGGTAATCTAGTGAATGAATACTTAACAAACGAATTCCCTAAAA
TCTAGATCATTAAGGGGTTGGGCATTGTACTGTGTCATTCCTAATGGCCC
AACACATAAGATTTTCTCACTGTTTGAATATTATCTGCTAATCCTAACTT
AATGTGTTATTCTACAGAAATACACACCATTAGAAGGAAATCGGTCAAAT
TTGGTCCACACTGCTTGGGCCACAATGGGTCTGATTCATTCTGGCCAGGT
CAGTTTGTAGTACTTGTCTTTATCAGACTTATGATTTGATTTCCACTTCA
GTATTTTGAATAAACAACCAGATCTACTCGAATGCATTTATAATTTAAGT
GATAAGAGTTCCATATATCATCATTCTAACCTATTACTTTATGTGTACGC
ATTCTTAGACTTGTTGATCAATTCTCCAAATATCATCATGCTAACTCGTG
AGTAATCCCATGTAGGCAGTAAGAGATCCGACACCTCTTCATCGTGCTGC
AAAATTGTTGATCAATTCTCAAATGGAAAGTGGTGATTTCCCACAACAGG
TATGAAACATGATTGGTTTAAGAAACTAAACTGATCTAGATACCACAAGA
TGAAGAAAGCAATTGTACTGCTGACTGTACATATGATTCCACATTTTCAT
GGCATAAATACATAATTAAAACTTGAAATAGTTTTGCACAAGCGTCTTGT
CAACTAATTATCCTTCAATTTCAACTTTAAATTATGCAATTATGTCTTCC
TTCTGAGCTATTCAAGAATGTTTTCCCGCTTATTTCTTTCCTAAATATAA
TTTTATATGGAGATGTATAAATGGTGTGGAAATATAAGCACAATGAAAAC
CACTGTTGTATCGTGCTGCATTCTAATAGATTAAGAAACAAAAATGAAGT
TTTGTGTACCTTAATTGTCTTCTTCCACTGTTGTCTAACCAGCTCACTTA
CCCATATTACAGGAAATTACAGGAGTTTTCATGAAGAACTGCATGCTACA
CTATGCAGCATACAGGAATATCTACCCATTATGGGCTTTAGCAGAATATT
GTAGGAATGTTCAACTCCCCTCCAAAAAGGTCTGATATCTACTAGTGGTG
CAAGTCCAGCACGACGGCCTCAAAAATGAGACGAGGCCAGAATCCTTACT
GCAGTCAATTTCTAAATTCTTTTGCAAAGGTTCGTTAAGAAAGAGCGAAT
TGATTGCAAATTCAAGAACCTCTTAGATTTATGCCACTAATTGTCCCCCC
TTTTCTCTGTACTAGTTGTAAATCACAGTTGTAATCATTGTCAACTTTCT
TTTATTAATAATGTATTATTATGGTTCATATGTAAATTTAAATCTTATAT
AGTGAAAGTTAGCAATGTCTATTCCTTTGTAACTTACAATATTCAGTATT
CACTAACTTAAAATGTGTCACAACTTTATTACTAATTTGCTATACTATAT
ACATTCACTATCCTTAAGGTGTGCTAAAAATTTGATGCTTTTATGCTTCT
TATTTAAATTACTAAATATACACTCTGAATGCTAAAGGAAGGTAATAAGA
GACTTGCATACATATGGATCATCCAGAGTAGGAAAATTATTATTAACAAC
TTAATTTAGGAAAAGTGAAAATTGTAATTGCAATACCATGCTATTTATGA
GTTCATATGCTCGAAATTCCAAGTAGCAGACAATGACGGAAACACTCAGA
AGCATAAAGCATGATATAATTGTGTAATGATTAATGCCATATA
Sequence Length: 
7793
Sequence Checksum: 
19666746b8681eb549845bc7d095bbe2
View location in JBrowse: 
DCARv2_Chr4:21393134..21400926-
Gene: 
LOC108218800
Gene Biotype: 
protein_coding
Gbkey: 
Gene