LOC108199318

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108199318
Identifier: 
LOC108199318
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017367087.1, is a part of gene, LOC108199318.
The genetic_marker, MK006438 K3882, is located in gene, LOC108199318.
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_017367087.1XM_017367087.1mRNADCARv2_Chr8:28551959..28559407
Sequence: 
ACAAGATTAAGCGAAAGCTGCACAGACTTCACTTGTTAGCTAAAAAATCT
CGTACTCTCATCTATACTGTGTGATTAAACAGCAAAACCTAATGATTATT
AATTATTATTATTCTCTTTTTTAATCACTCATAAATTAAAACCCACATTC
TAGAGAGAGAAAGCTAGCTAAAATCTGACACAGATAGATGCAGATTTGAA
TCACCAGCATTCTAGAGAGAGAAACACACACTCACGCGGCATTCTCGCTA
AACATATACATACACATCTACTTACATGTATAGAGAGTTTGTGTTGGTTT
GAAACCCTAGAGTGTTAGTGTCCAGATCCATGTATAATTGTACATAGAGT
GAGAGAGCGAGAGAGAGAGAAAGGAGAGACAGAGAGAGAGAGAGCGAGAG
AGATTTATCTGTGTTTGTGTGTGTTTTGATTAGAGAGAGAAAGAGGGAGA
GAGATTTGTTACTGTGTACTCGAGTGTGTGTGTTGATTTTGATGTGAGAT
TTGCAATTAGATCCGATATGGAGGATAATTACGGCGACGAAGGCGGAGTG
TCGGTGGCGGCGCGTGAGAGTAGTGGCGGCAATGCACGGTATCCGGCGAG
TGAGGTTACGCCGACGCCGTTGTCCTCGGCGTCGTTTAGAGAAGGAAGGA
GTTCGTCGAGACGGCGAGCGCCAGTGAGGCCGCCGAGCTTGGATGCGGAT
GATTTTATGAGTCTGATGCACGGTTCCGATCCGGTCAAAGTCGAGCTTAA
TCGTTTGGAGAATGAAGTTAGAGGTCAGGAATTTGTGGTTGATCTATTTG
TATATGTGAATTGTTGTTTGAATTTTGGCTTGATTTGATTAAGTGTTGGG
TTTAATGTGGTGGTTTTTGTGTAGATAAGGATCGAGAACTTGGCGAAGCA
CAGGCGGAGATCAAGGCACTCAAGTTATCTGAACGTCTTCGTGAGAAAGC
GGTGGAAGAGGTCTGTCCCCTATATGATTTGGTCTTATTGTGTTCAATTG
TATGTATATTATATTGTTTCCGAATTTTGGAGCTTAATTTAAATAAAACG
GGAATAAAGGAAAAAGGAGGATTTTGAAGCTCAATTATACAGTGTCAATT
TGAACCAATTAATGTTATATTTCATAACATAAATACACTGCATAAAGATT
GATACCACTATTTTTTTTCCTTTCATACTAAATTCCTACTTCAAGTCGTT
GAATACAATTGTGTTGACGTACTCATGTTGTGTATGTTTACCTTTTTTCC
TTTCATAATTTATTCGTATTCTTTGAGTTTACATGGTGTCTCTTTTTCAG
TTTCACAGTTGGTTTTCGTATGCCTGATACTTGACGTTATATTAAGATTA
TAAGCATCAATTGGATTTTATTCAGATCACAAGCATGACCCATTTAGACA
GTGGATCCTTACACAGCAGACTCGGCCTAGTTTAGTACTGAGCTTACTAA
ATAAGTAGGTGCATGCTTTTGGAAAAAATTACATTTGTTCTTTGTCATGA
TGACTCCCTTTTTATTATTCCAGCGAAGTCGTGGCTGATTTGATGCTCTT
AAAAAAGTAAATCCTAATAATGATTGTGTTTAATGCAACACTTTTAAGGA
ATCTTTTAGGTCTCTAGTTTTGTGTTGAATTGTAAGCTAGTTTATGGTCT
CTCAATTGGGAATGCTAAGATTTTAGTTAATGGTTTGTTTTTTGATATAA
TGGGCCAGGAAAGTTTCATTACCTTTATGCTGCTTAAAAATTATTACATG
GTTATTATGTTTGGCCTCTGCTTCTGCATACTGACCCTATGAATTTTCTG
GAAGTAATTTGTTATTGAAGCAGTAGTGGTGCAAATTAGATTATTAGATC
AATGGAAATTTCACGACATGGTAATGGAATTCAAAACTTTGCTCACTAGA
GAAGAATATAATTGCCGAACATTCTAACATATATCTATGCTCCTTATTTG
CATCGGAAATTCATGTGTGCATAATCTCCTCTCTTATTGAGTTGCAAGGT
CCTTGAGTCCTATATAACAGTAGATTGGTGTAGATGTAAAGTTGATAAAA
CATGATATTGTGCAATAAATTTAGTCCTTCGTTATGTATATATAAACAAA
AATGAAAAGATACCATATATTCTTAAAAAAAAATTAATAAACAGACACGT
TGATATGCATCACATGAATGTCATAACCTATTTTGGGACCTTTTAAGACC
CATACGCCTCAGGTTCATCTTGTTCGAAGATATATGTTGGTCCTGTTATT
TCTTTTATTATAGATGTGGAGTTGTAGCCAGACATAAATTTAAGCTTTCC
CTTATCTAGTTGCAATGTTGTAACAGAAGTGCGTGACCTTTTCTGTTAGC
TCCTGAAGTTATTTGAGTCATGATATTGGAGTTAAAACTTACATGTTGAT
GCGTCCATTTTTAACATAGCTAACTGAAGAACTGGAGAAGGTGGACGAGA
AGCTCAAGCTTACGGAATCTCTTCTCGAAAGCAAAGTATTGACTGAAGCT
CTACCATAAAGTTAATTTTTCCTTCTACAGTCACAAAATCTAAATGTAGT
GGGATCCCTCTTTCTTGGCAGAATCTCGAGATCAAGAAAATTAATGATGA
GAAGAAGGCCTCAATGGCTGCTCAGTTTGCTGCAGAAGCCACTCTTCGTA
GAGTTCATGCTGCTCAAAAGGATGATGATATGCCCCCAATAGAAGCCATC
CTTGCACCTTTGGAAGCAGAGCTCAAGCTCGCTCGTCAAGAGGTATAACC
ATATAACATCAAATTTGTTTAAGAACATTCAATTCTAAAATATTCTAATA
ACAGAATAGAAATTGCTCTTTTGAATATAGTAAAGTAGTTGACATATTGA
GCTTGTTATCTTTACAGATTGCTAAGCTCCAAGATGACAACAAAGCTCTG
GATCGCCTTACCAAATCAAAAGAGGCCGCTTTACTTGAAGCTGAGAGGAC
AGTGCAGGTTGCCTTGGCGAAGGCTTCTATGGTAGATGATCTTCAAAACA
AAAACCAAGAACTAATGAAGCAGATAGAAATTTGCCAGGTATTGTAGCTG
GAGTTCATCTTTACCTTTCCTAGACTTGAAGGTTATATTATCTGAATGCC
TCTTAACGTCTATTTGTATATCAGGAAGAGAATAAGATTTTGGATAAAAT
GCACCGCCAGAAAGTTGCCGAAGTTGAAAAGCTTACGCAGACTGTACATG
AGCTTGAAGAAGCTGTTCTTGCTGGTGGGGCTGCTGCAAATGCCGTGAGA
GATTACCAACGAAAAGTTCAAGAGATGAATGTAAGTTAATTTCTTGCTTA
ACCTTCCTATATGTGATTGTTATATTGAAATTTGAAAATGATACTTAATG
AACAAGTCTGTTTTTAATTGCTCAGGAGGAAAGAAAAACTCTTGACAGAG
AGCTAGCACGTGCGAAAGTAACTGCAAACAGGGTGGCAGTAGTTGTGGCT
AATGAATGGAAAGATGCCAATGACAAGGTGATGCCAGTGAAACAATGGCT
TGAAGAAAGAAGATTCATGCAGGCATGATAAGTTTTCTCATACGCTTGTC
TGAGACTTGGTCCCTTTCAGCTTATATATTCGATGAGAAAAAGTCTATGT
TGCTCTGTCCATTGTTATATCATATATGCTCGTGTAGTTTCTGTTCTTTC
TGCTTATTTTTGAATCCTCTTCTCACAGGGGGAGATGCAACAATTAAGGG
ACAAACTCGCTATAACCGAGCGAGCTGCAAGATCTGAAGCTCAGTTAAAG
GTAGCAGTTCCGTTTTTTATCTGTTATCAGTAACAATACCTGTATATCTA
TGCCATTGTTAGGATTCATTTCTAAATACTGAATTCAGGAAAAATATCAA
CTGCGGCTGAAAGTACTAGAAGAGACTTTGAGATCACCAAATGTTAGCAG
TCGCAACCCATTCGATCTACAAAGTGCTAGTCATGGTCGTCGTCAGTCGC
TTGGAGGAGCCGATAACATTTCTAAATTAACATCAAATGGATTTTTACCG
AAGAGATCGCCATCGTTCCAGCTGAGATCATCTGGAAGTAGCACAATGTT
AAAACATGCCAAAGGCACATCTAAGTCATTTGATGGTGGTACTCGCTCAT
TGGATAGGGGTAAAGTTCTAAACGGATCTGGTCCAAGTTTTAATCTTCGT
GATTCTTCTGAAGAAACCAAGGCGAGTGCTACATGTAATAATAACTGGAA
AGCAGATTCAGATGAAAAACCTAATGACTTCACAGCAGCACCAGAGAAGG
AGGATACTGTACCAGGATTGTTGTATGACTTGCTACAGAAAGAGGTTGTT
GCTCTGAGAAAAGCTGGGCATGAGAAGGATCAAAGCCTCAAAGATAAAGA
TGATGCCATTGAGGTCGTAATTTCTTCATACTGATACTAAGATGCTTGTC
TTATAGTTTTGTCATCTTATAGTTGTGATTTTCATTTAGATGTTAGCAAG
AAAAGTTGATACCTTAACTAAGGCAATGGAGGTGGAGGCCAAGAAGATGA
GAAGGGAGGTAGCTGCCATGGAGAAAGAGGTAGCTTCTATGCGTGTTGAT
AAAGAACATGAAAATAGGGCCAAGCGCTTCGGAGGAGGGGCAAGGGGTCC
TGCAAACAGTTCTCAGCTTCCTGCTAGGTATTTTTTTTTTTTGTTGTTCT
TCCTTTTGTTTGATATATATATATATATAGGGAAGTGCTCAAATACAAAC
TAAGTTAGTGTACAAACTACAAACTCAATATAAGCCCTTGGATGAATCTA
ATCCAATGGCCCCGCAGGGGCAACCACACACCAGTTAATATACACCCTGT
CACACATGATCTGCAGATTCCCCTCCGTTTTTAATTTAAATTTTCCCGTT
AATCGGTGAACTTTTTTTGAAATCCGACTTCACTGTATTTTTGTTCATCT
CGCAACGATCAATTTCCATACCATATGTGCTATATTTCGATTTGATTTAG
AGACTTTTTAATTTTAGTTTGTAGTTTGTACGCTAAGGTGGTTTGTACCA
GAGTAAGACCCTATATATATATATACAAGTGGACCTTGCATATTGGATCT
AACTATTAGGACTATCACACAAGGCTGTGATGATAGGACTCGAATCATTT
GTGCTGTGATGATAGAATTTGAATCATTTTCTTTGTTTTGGTTCTGACAT
GGAGCAGCATACACTGTAATGCACTTCACCAGGCAAATTTAAGTTCTGTT
TGTCTTAGCTTATAAAAGGCAGAAGTACTTTTGGAGGTGGTATTTATTTT
GCCTGTTCTAGGAAGTAGATAAGCTAATTCAAACACGCACTATCACAGCA
TGCGACTATTTTATACTAGCTGCTTGTCAGATTCATAAGATGCCTTGGTG
AAGGAGTTAACTAGTTTACAAATAAATGTGCTGTCCTTACTGTCTTTTGA
TTTGTTTCAAGAAACTTACTTTTTTTACAGCCAACGTTCATGGTAAAGGG
ATCAAAGAGCTCCTTATAATTGTTTGTCTATTATAAACTATTACGGGTCC
ATATAACATGGATTACTTGTTTCTTGTTAATGAAGCTGCTGTTTGCTTTA
AATTTTCTGAAGCATATAAAAATCCTGTTCACTTTGTTTGATTGAGGAAT
TGATGTTTTATTCGTTTGGTCTTAGGTAGATAATTGGTTAGTTTTTGTTG
CCAAGTCTTGGTCCACTGCATGTTGTTTTCCATCATAGGTCAATTTGGCG
CTTTGAAGCATGGGTGTGGCACCCAGTTGCTGCACTGTGCACCAGGTGCG
GTGCTGGTGCGGCTGGGTGCACCACCCGGCGTCTCCCAGCATTTAGGGTT
GGGGATTCACAAGGGTGCGGGAAGGGCAAGTTATGTAATTTTGCAGTAAA
AAAAAGCGCATCTTCATTCTTCGGCTCATCTTCTGTTACTCTTCTTCTGC
AAATATGTTTGTGTATACTGTATACACACACACACACACACGCACTGCAT
GTGTATGTATATAGGAGCTTCAGAATATATATTGATGAGTTGATGCTTTG
GTTTTTGTGGGCTGCTTTGATTTTGTATATTTACTTGACTTGGCTGTATG
TATGTATACTTTTCTGGTGCAGCTTTATGATGGTTTGATCTTGTTTTGCA
AGTTGCAAGTAGATATGTAAATTTATTTATGTAATCTGTATGTATTTGTT
TGCTGATGGAATTGATATTTAATACTTAATTCAAATGCTACTCTTTTCCT
AATTAAATATATACGTGATGTACAATTTTTAATTTTTTTTAACTGCCGTA
TCCGGTATCCCCCCTCACTAAATCCCCTTTATATTTTTTTTATACCGAAT
TCCCGTTTCCCATCACTCACACTCGTGCTTCATAGATTTGGAATACTGAA
TTACATATAAATTACTTAGTTCCGCTGGGCCAGTTAAAAGCTATTTGCCT
TAAAATTCCTCTTAAGAGATCCTTTTTTATCCTCCTTCCGTAGATAGTGT
ACGAGGGAAATTCAAGTTCTAATCAGGTGGGTGTTGTACCTACTGATGGT
TTAACAGGAGGCTAGCATGAGTTTAATAAGAAAGTTAGGCTCACTTTCTT
CTCACACACACATACAAGCTGATTTAACAAGACTTGAACTGCAACCATTG
CAAGAATCAATAGGTTACTTTCTTGCTTATCACCAAGTTGCATTGCTCGA
TGTTCCGCTGCACTTCTTATTTTTCTAACTCCAATATTCCCTTGTATTAG
TGACTTGAAAGGCATTAGCGGAATGTCTTAATATACAAGCAGGTATATGT
TAAGGGCATAAACAATAATGACTGGTAATATGAAAGGAAACTTCTATTTT
TTACTTCCATAAATTTCTTTTTTGAGCTTTATTTACCCTTTTTGGTTTGT
AAATACCCAATAATGTTGTGAGAAAGATGTTGGAGCTTAATTATTCATTG
TAAATTGCAGGACTGGAGCACGAGGAGGGTTAACACGCAGCACCCAATAA
CCAGAAATCCTGATTGCAGCGCAGCAAAAAATAGTTATGCATAGCTTTCT
ATTGGGTCTTGAGCTACTTTCTCATCTTTCCTACTATTGACTTGTGGTTG
ATTTTAGATTACTTGGCATGCTATTGGTCTGGTATTTGATCCAGCATCGA
ACAAGTGATCAGAATACAATGAATAGGAGATAAGTCTGTGGAATCAGTAT
GCTTACGACGTAGTTCATCATCCTCCACTTGCTATCAACAAAGAAAGAAC
TGGAGGATGTTGTGTTTACTAACCCTTTGTCAGAATTTATCTGAGTGGAG
ATATTTGTGGATGTATAGGTTAAATTATTGGTGTTGCTGATATTTCACCT
TACGAGTTTGTGCTTGCAGTCTATATTTGTAACCTGCGGCTAGTTTTTTC
TTCTTTTCTTCTTTTGTTTTTTGGTTTTTAAATTGATTAATGTTTGTCAA
TATTCTCGTTATCTGGTATAAACTAGTAGCTCCCATGATTGTGTTATT
Sequence Length: 
7448
Sequence Checksum: 
111869575e716ff25e8263f76a3a4fe1
View location in JBrowse: 
DCARv2_Chr8:28551960..28559407-
Gene: 
LOC108199318
Gene Biotype: 
protein_coding
Gbkey: 
Gene