LOC108204254

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108204254
Identifier: 
LOC108204254
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017373605.1, is a part of gene, LOC108204254.
The genetic_marker, MK002861 K0305, is located in gene, LOC108204254.
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_017373605.1XM_017373605.1mRNADCARv2_Chr1:15366757..15375597
Sequence: 
GAGCGGAAGCGATGAGATTAAGGAGTGTAGTGTAATAACAGTGGAAAGGA
AACAGAAACCGAGAGCAGCAACATTTAAATAAATCTGATAAACCCCTCTT
CCTAAGCTACTTGTTGTCCAAAACCCTAGAATATCTCTGTCTCTATCTAT
CTGTATCACTAGCACACGGACACAAATATCTTGGCTCTCTCTCATCGTAG
CATGTCCTCCTCCTCCATATGGTTAGGTCTAGTAGTAGTAGTGGTGGTGT
TGTTGGTGAGCAATGCGGCGTCGTATTCTAAGTCCGAATCTTCTAATTCA
GGGAGTAGAGGACCCCACATAGCTGATGTGAATATATTGTTGCCTCCCAA
GATGACTCATCCTGTTCACTATAGACTTCAAGCAAGTGATGGCTGCTTCA
AATGGTATGATACCCCCAATTTTTTCTTTATTTCATCAATTTTTTTTTTT
AAATATTTAATCTCACTTGCTTACTTAACTTACAACAACATTCTACAACT
TCAATCTCAATTCTTATATGTGTTTAGCTATGTTTTACATCGGGACCGTA
GGAGTGCCATGCTTTCCTATTTAATTCACTTCTCTTTCCGCTTTCGAGTG
TAGCTAGAACACCTGCTCAACTATTGCTGCAGACTGTCTGTTTCTGTTGC
AGTGTTTAAGTAATTTTAAACTTTATATATGTATATAATGGATCAGGTCA
TGGGATCATCATGATATCTTGTCTGTTTTACCCGAGTACAATTCGAGTAA
TCACTGCTCCACGAGTGCCCACTTGAAGTCGATAGCACCCTATAGTGGGC
GCAAGGAGACGGCCGTGTATGCTACGGATGTGGATACTGGGAGGGTCATT
CGTTGCAAGGTTTATATTGATAATGTTTCTAGAATTCAAATATTTCATAG
TTCTGTCAAACTTGATTTAGACGGGCTTGCCACTTTACGTGTTCGTGCCT
TTGACAGCGAAGGTATGTCAAGCTAGTTTATGACTTAAACATTGAAACTT
TTTTTTTTCTTTCCATTGTATTGTATTAATTCATGTAATTGCAAACAACA
TTACAAACTCGATTAAGCTATACTATTTTTTTTAAGTGTCCTATGGACTA
TGGTTAGGGTCTCCGTAATGATTGATGCATCCAATTCAAACTTGTTCCTC
GTATCACGCACTTTCAACCATGACATCACTAACTGCTATCATTATACTAA
ACTTGACATGCTGATTGCTGACTTCTTATATTAATATATATAATCATGTA
GCTTTCTTGCTTCTTATGCTTTCTATGTTTTGTGCCTCTGCTGAACGCAT
GACATAATTCATTTGTAATTTGTATCATAATGCAACATTGACATGCTTAC
TTGAATTGAAGTGTTAAACTGTGCGGTGTATTATTATTAATTCTTGACAT
GTAAAATTGGTAAACCTTAGCTAAACCAGCATTTAACATAACAGGAGGCA
GATTGCTGTATTTTCTGTTAAATAAAATTGAAAACGAACGGGGTCAATTG
ATATACTGATCCAATCAACCATTTATATGAATTAATCACTAAATCTTCAA
TAAAATAAAACAGTGCATTAGTAAATCTTTGATGGATATGAATATATCAG
AACAAATCTATATTATTGCAATAATTGTTCTTGTTTCTGTGCTGCTATTT
TTCATTTGCATCATTGTATGTATAGGATGCTTAATGACTTGCATCACACT
ACTGCAGTTGAACTTTTGCTGTCAAGTGTGCAATTAGTTTACTAATTCTC
ATTTCTCTTGGCCTCTTGGGTCTATTTAGTAGAATATCAAATTTCTTATG
GACATTTTTATCAGTTTTTGTTATTTTTCACATGGATTGAGCTAGAAATT
AAATACTGCAGGGGGCGAATTTTTTTCCTTTTAGCAAGTAATATGGAGTA
ATATTTTATTAATGTTAAAAAAACATGTTAATTATTACAAATGTCATTGT
TTACAAATATGCTTGTAGCCTTGTATTTATATTAACACCATAATACTATC
GCTATATTCATAAAATTTACATATGTTTGAGGGGGCACAAATATATACTA
AAACATTTTAGCATTAATATATATATATATATATATATATATATATATAT
ATATATATATATATATATATATATATNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNTATATATAAATAGGCCAACATTCCAG
AGAGAGAATCCTTATGTGGAGTTACATAGTGCGCTACTATAAATTATCAA
TTTTATTATAAATTCTGTTATAGAATACATATAAAACGTGATTCTAATAT
AGAATACTATAAAATAAATCTATTTTAAGTAATTTAACACTTAAAATTTG
ATTAAAAAAGTATATTTTCGAAACTGATTCTACAATAAAATAATTCTGGA
TGATTATTATTCTGTTATAGAATCATGTTGAGATATTGCATAATTTTAGA
TGATCTTTGGAATAAAAAAATTGTATAACTTCGTTTTCGGTTTAATAATC
AAAATTTGTAATTATATTTCATAAAAAATATAATAGAATATATATTATGT
ATATATTTATAATGGTGTGCTACGTAACTCCATATAAGAGGGTATGCTAT
GGAGTGCTACCCTATATATATATTGCTCCTGAATTTTATACTAATTTTAT
GGCTATCGAATTTTGGGCGGCAGCTGGCACCATCAGCCACCCCTTGCCTC
CATCTTTGATTGTTATTTATATTGTTTAGACTTTAGTTGCATGTGTTCTT
GGGGCTATTATGCTTGCCGTGTCTCTGAACTGATGTATTTTTTATTTAAC
TAAGATGTGAAATTATAAAAAAGCTCATATATCTTTGTTTACTGTCTCAT
TGTGCAGAAAATGTGTTTTCATCCCTAGTGGGCATACGGTTCATGTGGCA
ACTCGAGCCTGAAACCGATGAATCAGCTCATCACCTTGTTCATGTACCTT
TAAAGCTCTCTCCACTAAGTGATTGTGGTGGCTTGTGCGGTGATCTCGAC
GTCCAAATAAAGCTTGAAGATAGTGGAGTTTTTTCAGACCTTTATGTTGT
AAAAGGAACTGAAATCGGTCATGAACGCGTTTCAGTAGATCTGCTTGAGC
CAATGTATGATCAGATGGCTGATAGTATTGTTCTAACTGTTGCAGAAGCT
ATGTCTCTTTATCCACCATCCCCTGTTTTTGTTCTTGTTGGTGCTGTTGT
GCAATATCTACTAACAGTTGTGCGCGGGAATATTCCTCGAGCAGTAACTT
TACCATCTCCGTATCATCAATGGTCGGTTTTGAATTCTTCAGTTTCTCGG
ATAGACAAAACGATGGGTATAGCTCATGCACTGAACTTAGGTGTCACAAC
TGTTAGTGTTGAAGATACAAGAGTTGCTGGTCACATCCAACTGTCATCAC
TACATGTAGTGCTTCCAGATTCTTTATATATATACATATCGCCTTTGTCA
CATTCTGGTGATATTCTCGAAGGTGCAGCACCTAATCCATCTGTTTCACG
TTGGTATGTTGTTACTGGTAGACAATATCTTCTTGAAATGAAAGTTTTCT
CGCGAGTACCTGAGTCACAAGAGATATATATAACGGAGACTGATGATATA
AAGTTGTATGATGACCATTCTGAGTTTTGGAATATATTCCCAGTTTCAGA
TACTACTACTTCCAAACTTGTGTGTTTGAATTCTAAAATTCTGAAAGCAA
TGTCATATGGATTGGGTAAACTAACTGCAACTTTAACCTACAGTAATGGG
GTTCATGAGGTGAATCAGGCTCTCAAGGTTGTGCAAGAAATCATGGTTTG
TGAGCAAGTAAAGTTTAGTAAGGACAAAAGAAGTGCATCTGGGAGTATTC
TCCTTCCATGGGCCCCTTCTGTCCACCAGGAGGTGGAGCTAAAGGCAACA
GGAGGTTGTGCCATATCATCCAGTGACTACAAATGGTTTTCTTCAGATAT
GTCCATTGTGTGTGTATCAGCACATGGTATTGTTCAGTCAAAAAGACCAG
GGAAAGTTACTATTAAAGTGGTATCTAGTTTTGATTCTTTCAATTACGAT
GAGTTGGAAATTGAAGTTTCCATTCCTTCCTCTATGATCATGCTGCAACA
ATTTCCTGTAGAGACTGTTGTGGGATCAAATCTTGCAGCTTCCGTGACAC
TTAAAGATTCTAATGGTGATAATTATTTCAGATGTGATGCTTTCAGTTCA
GCCATACAGTGGAATACCGGAAGCGATTCTTTTACGATTGTCTATACAGA
GAGAGAATCATTCTTATTTGATGAGCAAGACGTCCCTGATTTGCTTGCAT
CATTATATAGCCCGCCATGTGCCTGGGCCCGTATATATGCTTCTGCTACT
GGGCGAACAATGCTACATGCTTCACTTAAAAAGGATTATCATCCTCTTGA
TCATTCGCTCACCGGATCTATCGATTTAAAAGCATCAGCTCTCATTTCAG
CATATCTACCACTCTTCGTGCATCAGGCAGGTGATGGGAACCAGTATGGT
GGTTATTGGTTTAATTTGTCTTATGCTGAGGCTAATAACCATTTAGAGAA
TTTGAAAATCTTGAATCTTGTTCCTGGCACACATATGGATGTCACTCTGT
CCGGGGGACCAGATCAGTGGGGAGGAGGTGTTGAATTCACTGAAACTGTG
GAAATTTTACCTCAGGAACAGACTAAGCAGAAAGGGGTTTTGGTCCATAA
TATAACTACCATTTATGGTAGCTCATATAGAATATCATGCGAGAATTGGG
GAGAATTTAAAGTTCTTTTCAAACGTGGAAACTTGGCTGGCGATGATCAT
ATACTACCTGCTGTGGCGGAGGCTGAACTATTGCTCTCATGTATCTTACC
ATCTTCAATCTCAATAGTAGTTGATAGTTCTGTCAATGCCCTTGATGTGA
TACACACAGCTATGCAGGCTGACCGGAATTCAGAGCAAGTTCGGGCCCTT
CCAATCACTGTGGCTAATGGGCGAACTATTAGAGTATCTGCTGTTGGTAT
TAGTGACTCTGGGAATGCTTTTGGGAACTCTTCTTCTCTTAGTATAAGTT
GGGAAGCGAGAAATTGTGATGGATTGGCCTTCTGGGATGCTGCTGCTACA
TCCATATCAAATTGGGAGAGGTTTTTGGTCTTGCAAAACTCAACAGGACT
TTGCACTGTTCGTGCCACAGTTGGTGGATTCATAGAGACCTTGAGTAATC
ATCGCTTTATTAAATCCTATGGAAGTTCAAAATCTCTTACCGATGCCGTA
CAACTACAACTTGTCTCTACTTTAAAAGTCACTCCAGAGTTCAGCTTGTT
ATTATTCAGTCACTTGGCTATATTAGATCTCTCAATTAGTGGAGGGAGTT
GTGCACTGACTACTGTGGTTAATGATACCCAAGTTGCAGAATTAATTGAT
CGTACACCAGATTTGCATTGCTCTCAACTATCACTAGCGCCTAAAAGTTT
AGGGACTGCACTTGTTACGGTTTATGATATGGGACTTTCTCCCCCACTTG
CTGCCACCTCCGTGGTTCAAGTTGCTGATGTAGATTGGCTTAAGATTACT
TCGGGAGAACTAATAAGCCTCGTGGAAGGAAGTTCCCAATCTATAGATCT
TCTGGCTGGGGTAAATAATGGACGCACTTTTGACTTCTCCCAGTACATGT
ATATGAAAATTCGTGTGCATATTGAAGATCATAATATTGTTAGTCTGTTA
GATGGTATTAGCGATGGATATCTGAAGGCTCCAAAATTTATCCTTCAGGC
CAAAAATCACGGTATTACGACTCTTTATGTAAGTGCTAGGCAACAATCTG
GACGTGAAATATTGAGCCAATTTATTAAGGTTGAAGTTTATGCCCCACTT
AGTATACGTCCTTCTAATATATATCTTGTACCCGGTGCTTCTTATGTGCT
TACCGTGGAAGGAGGCCCAACTATTGGTGGTTATGTTGAATATGGAAGTA
TGAATGATGAGACTGCAATAATTCATAAATCTTCTGGGCGGCTGATTGCA
ATTGCTCCAGGGAATACAACTCTCGTGGCTAGAATTTATAGCAAAGGTGA
TGAAGTGATGTGTCATGCATTTGGATATGTAGTAGTTGAGATCCCTTCTT
CAGCAATGTTAAATGTGCAGAGTGAGCAACTTGCCATTGGTAGCGAACTA
CAAATATATCCTTCGTTTACCAACGGTAATTTGTTTTCTTTGTATGAGGT
GTGCAAGAATTATGAATGGAGCGTTGAAGATGAAGACGTATTGACTTTCA
AAGTAGTAGATCTCTTGCATGGTTACAAGCTTGGTGCCTCTTCCATTGTT
TTGGAAGCAAGTGGATCTAATGAGAAGCTTGACCTAAGGTTTATCCGCGA
GTTTTATGGAAAGTCTTCTGGCCAGACTCATGTCAGCGTTTCATTTTCTT
GTAATTTTGTATCCCGTTCATTTTCACAGTCCAGGTTATATACTGCATCC
ATATTGCTCTCTGTGGTGCCTGATCTCCCTCTTGCTCTTGGAAAACCAGT
GACATGGGTACTTCCTCCTCATTATATAACATCAAATCTCTTACCATCAT
CTTCAGGGTCCTACAGTCAGGGAGATGCTCAGAGCAGCAAAGGAACCATT
ACTTACACTTTGTTAAAAGAATATGGGGGTCAGAAAGATATAGAGTTGGT
AAATGAAGCAATATCCATCCAAGGTGTTAAAATACAAACAAGAGAGAGTA
ATAATATTGGGTGCATTCAGGCGAAAGATAGATTGACTGGAAGATTTGAG
ATTGCATCTTGTGTTAGAGTCGCTGAGGTAGCTCAAATCAGAGTGAGCAG
GCATGCGTTTCCATTTTACAGCGTTAACCTTGCTGTTGGAGCTGAACTCA
GTATTCCGCTGATATATTACGATGCTTTTGGATACCCTTTCTACGAGGCT
TATAACATTGTTTTGTATGATGTTGAGACTAACTATGGCGACATTGTCTC
CATCAATGACACACATGACGGTAATATATATCTGAAAGCATTACAATTTG
GTAGAGCACTGGTCCGAATATCCTTAAAAAATAACTCAACCAAGTCGGAC
TACTTGTTGATCACAATTGGTGCTCGTTTGTACCCTCATAATCCACTCCT
CCAATTGGGTAATCGTCTTAATTTCAGTATTGAAGGCCTCACTGATCAAG
TATCTGGCTGGTGGACGAGTGTTAATACAAGTACTGTTTCAATAGACAGG
GTGTCTGGAGAAGCTGAAGCCATTGGGGAAGGAAGTACTCAAGTCATCTA
TGAAAGCTCAGATTTCAAGTTGCTGACGTTTGTTACAGTCTCAAAGGGGC
ATATGATAACTGTTAATGCTCCAAAAGGGATTCTAACAAATGCTCCTTTC
TCAATGAGAGGTTATAAATTCCTTGTGACATTTAGTGATGCGTTTGAACC
CATCCGTGAACCAGGGGGGGCTGTTAAAACACTCCTGCATGAGTGTGAAG
TGGAGCCACATTTTGTTGGGTATGCAGACCCATGGATGGATTTTGAGAGT
GGAATGTCATATTGTCTCTTCTTTCCATACTCACCAGGACACTTGGTTCG
TTCAGTTGGAAATTTGAAGGATACAAGGCGGGATATAAGTGTTACCATCA
ATGCTTTTGTGCGAGGAACAAACAATATATCTGGATCTGCTTCTGCTTTT
TTTGTTGGTGGATTTGCTATACTGGACATGGACCACAACTCATTACATTT
GAATTTGACTTCCAAGTCTAACAAGTCTGTCATAACTGTAGTCGGTAATA
CAGATGTTGTTGTTGACTCGCAAGGTCGGAATCAGTTGCTAATCACACCT
ATACACAGAGAAAATAATGGAGTAGCAGGGCGGGCAGAATACGAGGTCAA
AGTTCTCAGCTCTTGGAGGTTCAAAGATAAATTGATAATTTCACTCGCAG
CAAATGGCCAGAGAGTCGAAATTGATGTAAACTATGAACCTGAGAAGATA
CCCGCACTGCCTTCATCCACTAAAGTCAGCAACTGGATGGTTATACTTGT
GTGTTCCTCTGTTCTAATATCAACACTAATTCTGTTTCTCTGTTACCTGG
ATAGATCAAATAGATATCAAGCAAATGCGGCACCTACCACCCGAACTGCC
ACAGTTCAATCACCGGCAACCCCTCCTCGGAGCAGTCCATCCGTCGTGAA
TGAACACTCTCCACAAACGCCTCAAGCTTTCATAGACTATGTAAGGAGAA
CAGTTGATGAGACTCCTTACTACAGGAAAGATCCGCGCAGGAGGTTTAAT
GCACAAAATACCTTTTAGATTGTATGAGCACTTTATTAGTTCTCTCCTTT
CCCCTTTCCCCTTTCTAAGTTGTTGTATCAGTTTGGATGAATATATAGTC
ACACTAGAAAAGGGTTGTAGTCATGTAAGGCAACTGTTGTATTAATGCCA
TTTTTCTGGCTACAAATTTAAGCCCCACCCTTTTGTGCTC
Sequence Length: 
8840
Sequence Checksum: 
fafc12589d2e7a86bdef9bae44258a53
View location in JBrowse: 
DCARv2_Chr1:15366758..15375597+
Gene: 
LOC108204254
Gene Biotype: 
protein_coding
Gbkey: 
Gene