LOC108225774

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108225774
Identifier: 
LOC108225774
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017400728.1, is a part of gene, LOC108225774.
The genetic_marker, MK004759 K2203, is located in gene, LOC108225774.
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_017400728.1XM_017400728.1mRNADCARv2_Chr6:17763335..17770847
Sequence: 
TGCTGTATTGCAGCAGCACTTAAAAAATAAAAAAAGAAAGAAATTCAGTT
GTGAGCAAGTCTCAGTCAGTCCTTGAACACACTCTCGTGATATCTCCATA
ATTTAACTCAAAGATTTCTAAGTCATGCAAACTATTTTGTTGCCGGAATT
TCGTCCCACCTGTATTCCATCTATATTTACGGCCAAATCCTCGTCACACT
CTCGCCGTACTTCATCTTGTAGCCATTCAATTTCTTTCAGCCGCAACCCC
TCTCACTCATTCTCATCTTTCTCTACTCCCCTCAAAATTCAATCTTTATG
TGAAATTCGATCAAATCAGAGGAAAATAACACCTGGGGTTGCTCCCATTT
CTTCTGTTTATGCACCGCCCTCCAATGATGAGACAGAAGATGCAAAACTA
GCTCAGGTCAATTCTTGGTTATTTTTATTTTTGTTTTGCATTTTTGTAGT
TTCTTTAATATTTGTGTTAGGTATTAATGTATAGTTTATACTGTGAATTC
TGGGTTTAGGGTTTAAATGAACAGTGCGTGCTTCATTTGTTGTGGATTGT
TTATACAGTTTTAGCATTGTGTCATTTTCTGATTTATGATTCAAATAATA
CATATGTCTTGGACACAGACATGACCTCTACTTTATTTCTTCAAGTGGAT
ACATAGATTGTTCCTTAAAGACCCTTTATTTTAAAATTTGCAATTGTGTT
GTTTTATAGCTGGAGTGAGGTAGACTAATGTGGAACAATGAATACCATGT
TATAAGCTCTCCCAAAGAGGTATGACAATCTGATTGCGATCATTAATCTC
TAACACTATATTTGTCAACTCAAAAAAGTTTGACATTTTTGTTTAATGGT
CAGCAAAATTAAGAAAAGACATTGTATTATTAATGATTGTTTAGCTCCAA
TTACAAAACTTGCACACTTGTGAAGTTCTTTCATTCATTTTTATCTTGTT
ATTATGTGAAAATATCTCGAGTTCATTTATCTTATGTTAATGGATACTAG
TCAATTTGTTATGCAATTTAAAAGAAATATTGCCTGCCTTTAAAGTTTTG
GAGAATAAGAGGATAATATAGTTAATGTCTTTCAAAGTGGTTCAACATTG
AAAGGTTTTAACTGTTGTTGTAGGTCGCCAAGAGATTACAACAGACTGCG
AGGTATTTCAAGAGGTTGGGTAACTTGGGATTTTGGGGACAGCTGGCGTG
TACTATAGTATCTGCTGTTATTCTTTCTTTCTCGATTGTTGTTACGGGAA
AGATTACTTCACCTGTTACATTCTATGCAACTGCTGGTGGTATTGCAGCT
GCTTTCATTGCAGTGTTTTGGTCGTATGGTTATATTCGTCTTTCTGATAA
GCTACAAAAAACTGCCTATAGCCCTTCCAAGGTGATATCTTTATTTTATA
TTTCTTTTATCATTTTTCAGAAGATCTCAAATATGTTGTTAGATGTTAAT
CATTTCCTTGTTTATAAGTTGGCTAACTCACTCTTTTTAAGTTGTTTCTC
ATGGATACATTTCTGAATTTCTTTTCCTCTTGATCTAAGTTACTATAAAA
TATAACATTAAAATTTAGCATCGATAGTTCAAATTTAAATACTTTGTCTA
GTTTTAAGCAAGACTTAAACAAGACTCGAATATTTGAAGTTTGAATCTTC
AAGATATACAGCATTAGAATAGGTATTTTTATTAGCTAATGTTTAATTTA
TGGGTAGATAAGCTAAATCATCATTGTACTATACTGAAACTTTCAGTTGA
ATCACCAACTCAAAAAAGTTTTCAGTCAAATACTTATTCAATGTAAAACT
TTCATATAGGTTTTCACCGTTAATACTGTTAAAAATCTTAACATAAAAGT
GACATGGCAGCTATTAAGTTAATCTTTATCATCTCCCTCAATGTAAACAC
AATCTAGCATATTTGCATTTCAAACTCTCTGATAAAAATATGTTGAGTCG
CCCAAGTTAAATTACTGTAGTTAAATGATAAAAGAGGATGTACAACTTAG
ACTACACCCACATGTCAAGTCATGTTACTCATCTGCTTTCAGTTAGCTAT
AGTATGCTTGGGATCTCAATTTTTAGGAACAAAACAATTTCTTATAGCAA
TACAAAAGCACACTATGACTAGACATACAAGAAGTCCCAATGACTGATGA
CTAATCATAATGAAAGAGGAATATAAATTCTAATACAAGAGAATACATAG
CATAATATGCTTGTTTGTGTGTCGCGGGCTGCTACAGGACTCTTTGAGTG
GACGCAAGTATCAAATATCTGCTAATGTGTCTTTATTTCTATTAAATATG
TTGAATTTTTGCTGGAAACCAAATATTTGTTATGTCAGGCTCCTCCCCGT
TCTGATGTGGTACAAAGCTTGAAAAATGGCATAATTGTGAACCTTCTGGG
AATGGGTGCTGCTATGCTTGGCATGCAAGCTACTGTAGGGTGGTTGATGG
CTAAGTCTCTGACCACATCAAGCAATCCATTTTACCAAGGTGTCTCACCT
ATGAGCAGTCCTGTTCTGGCGTTGGATGTGTTCTTGGTGCAGGTACTTCT
CAAATTTTTCTCCAAACCTTTCAGTTCGATCTTATTGGTTTTGTATATGA
ACTTTAAAGATTCTTCTAGAAGGCAATTATACATGACAAAGGCAAGCTGC
ATTGGTTTTTACCATTATATGAGGTTAGGTGCCTTGGGAAGTTAAGATTG
ATTCTTAACTCCCAAGGCTTATACTAAAAAATTTATATTGCATAACAGGT
AGCTATTTAACAAGGTTTTTTCAAAGTTCAAGTTAGATCATGTGACCAAA
GAATTGCATAATACTGTATATTATGTTTAAGGTGACAAATTACTTGACAT
GAAAATATTCCTTCAGCCCCCTCCGATTTCTTGCTTCACTTATTTGCAGC
ACGAAATACATACTTTTAATTAAGAGGGGTCATGTTCCAGAGAGAACCAT
TAGAGAGAGAACCATAGAACCCTTAAGCAGAACTTAAGTATTAGTTAGGG
TTCTGCAGCAGAACTTCACATGCAAAAAAATGTCAAAATCTATGTATTAA
GTTTAAAATTATTTTTGAACACACACAACGATGAAAAAACATGAAAAAAA
CATGTATTTAGATTTAGATCCTAAAAATCTATTTAAAATTTAGGGTTCTG
CAGCAGAACCCTAGTGGTTCTATGGTTCTATTTTAAGGACTGGTTCTCTC
TTGAGCGCGACCCTTAATTAATAATCTGTTTGGTAATTGTTGTTTTGCAT
AGATGTTTAGGAAATTAATTATTATGACAAATAAAATTTACAAAAATTTT
CAGATTTAAGTCTATTTATTTTAAGCATTAAAAAGTGCACAAAAAGTCCA
GAGACGAGAAAAAAGGAACATAGTGAGTACAAGAAATTATTAATAGGATA
AACATGAATTAGATAAGCTGTAATAGAGAATGGAAGTTATAACGTCTCCG
AGGGTGGGTATCTATTTGACTCTCAAACAAAGTAAAATTATTGGCTAACC
AAAATTAATGTCTTGCTCCAACCATGCTAGATAATTGACTATCTATTTGA
TTTTATTATTATTAAAAAAAAAAACTAAAGAGAGGGGAGGGGAGTAGAAA
GACAAAGATTGAACAAAAAGTGGAAATAGCTATAATTTTCGTTATTGTGA
CAAAAGATAAATTTGTTGACAGTTCTGGGCTTGCTCTTCGATTGCTAACT
AATCTCAATCTCTCTATGATTGTTTTAACTTTACATTTTAGCTAGCTATC
TCATGCTTGTGGGAATGGTGCATGTCTAAACTACACAAACTTGGCCATTT
CCAGAGTAGAGAAGTAGGGGTGTGCATGGTGCGGTTTGGTGCGGTTCCGG
ACATTAACCGTTACCAAACCGATGAATGCGGTTCGGTTCGGTTAATCATC
ATTAACCGTAACCGCACCAATTAAAACGGTTTTTCGGTTGCGGTTAACCA
TTAGTCGGTTGCGGTTTTTTTTTGGTTTTTCCACTATTATTTGCTACTCT
TGTGCATAATGAATTTTTTAAAAAAAATATAAAATTTTCATGAACATGTA
CAATATGTTCGGTTACTATTTACTATTGTTTCTATATAAGGATATAGGAA
ACATTACATACTTTCATCTAAAAAAACCTTAATACACAATAAAAATTAAA
ACATACGTATTTTGACAAGAAATTAGATGATGTCAAGTCAATAAAATTAC
CCAAAATCAACTAATCATGAAATTCAAATAAAAAATGTTCAAAAAGTACA
TAAATAAAAAAAGTAGAATAGGTTTCATAATAAAATTTGATCAGCAGATT
AACAGCAGAAATATTTCTGCTTTGTGGCAAATCACAATAGCCCTAGTTTT
CGATCAAGCGCTCCTCCAAATATTTGGGTGCCCGGTTGTTTAAGTGACTC
AGCAAGTATGCAAGTACGAAGAAGATACTCCATATAAAATTAGATGTGAA
GTTTTAAAATGACTAAAATGCTTTATTACTATTAATATATATTCCCTCCG
TCCCACCCATTTCTTATCGAATGGGTTGGGCACGGAGGTTAAGAAATATG
TATAAAATAATGGAAAAGAGGAAGAAAAGTAGGTAAAGTGGTGGGACCCA
TTGATTTTTAATGTATAAAAAGTAGATAGTGGAGTAAAAGTAGTGTGAAA
AGAAAAAAAAAGTGGACAAGTGGTGGGACCTATTGACTATTTTTGGTAAG
TTTTGAAATGTAAAGAATTGGATGGGACACCCCAAAAAAGAAAGTGTAAA
GAAATGGGTGGGACGGAGGGAGTATATATTTCGGTTCGGTTAATTTCGGT
GCGATTTTAGTATAAAACCGAAAATAAAACCGCACCATTAATTTCGGTTT
TTTATCTCGGTTATTTTCGGTTTTATTTGCGGTTTGATTTTTTTCGGTGT
GATTTTTCAAATTTTTTAGGTTTTTTTTGCGGTTTCGGTTTTTCATGCTT
ACCCTTGGGCAGACATGAACATATACATGAGGGACAATGGGAGTGGGAGT
TGGGACTTGGGACCATATAGCACCTGCTCATATAATGTGACGATAGTCGA
TAGATAACAGTGTTTAACCTTTTTAGAAATGATTGATGCAAGAGCTTCCT
TTCTTTGATTGGATTTGATGTACAGCGAAGTGGCGGCTAAGGCGGAATCA
TACTCCTTGGATTCATTTGTGATGGCATGCGCTTTATTTATTTTAATCTA
ATAATTGATTTACTAGTGACAACTTTTTCCTATTACCCATTGCCCATTTC
ATTTTTGGTTACCTCTCAAATTTTGCTAAGATAGTTTCCTTCATTAATTA
CATACAGTAATCTTCTAGCTTTAGCTAAAAAGTGGTGACAGATTATATAA
TTAATGGATTTTTCTAGGGCTGGTTAAGAAATTTGTTATAATTCAGCCAA
CTGAGTTGCAATTCCGATTATAAATTTAAATTTTATGTTATTTTTTTAAA
ATTAATTTAATATAAGTAAAATAGATGACGTTAATAAGAAATATATTGAT
ATTTATAAGTATAATTGTAAGAAATGGGGAACTAGGATTAATCGGCGGAG
ATGGTAATTGAAGATAATTAATGGGATGATATATGCATTAATCATAAAGA
TTAATCGGATTACGGATATTTTATAATATTATAATAATATTTGAGATATC
ATTTTAATTTATTATATAATATATTGTTTAAAAAAGTTATAATAACTATC
TTAAAAAATTATAATAATTAATCAAATTTTATAAATCGAATCAAAACATC
GCGAGAGATTAATCGCATAATATTAATCTCAAGAATTTTATTGAGTCAAG
GTAAAAACACTTTTGATTGAGGTGAATAATTCCGGAAGAAATAGAATGAT
AAATGAACTATATTACGGGGAATTGTTAACAAATTTCATTCCTTCCATTT
CTTACATTAAGTGCTAGAGATCATATCTTCAATTTGAGATAAAAAGCTCT
ATTCTCTCCTACCCCTAATTTCTTCTCAAATCTCATCATAGCAATTTTGC
ACTCACTTAAATTTATTTCAAAACTTCCCTCCTATCTCTATTAGTTCCAA
CTATTTTTACTCATTCCATTCCATTCTCCCACCAACCAACAACNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGAGCCTAGGTTTAGAGTC
CCTGGACAGCCCAATTAGGATCATAGGGTGTATAAGTATATTATATATAT
ATATATATATATATTTCGGTTCGGTTAATTTCGGTGCGGTTTTAGTATAA
AACCGAAAATAAAACCGCACCACTAATTTCGGTTTTTTATCTCGGTTATT
TTCGGTTTTATTTGCGGTTTGGTTTTTTTCGGTGTGGTTTTTCGGTTTTT
TTAGGTTTTTTTTGCGGTTTCGGTTTTTCCTGCTCACCCCTATAGAGAAG
TACTTAACAATAGATTGTATAAAAGTTAGACTATTTGAGTCATAAATTGT
TGGTTTCCAAGTATTACAAGTAGGACAAACCATCTCAGCATTGCTGGCAA
TATAGTTGCTAATTCATGCTTTGTAATAACAGGCATCTGCAAATACCATC
CTGTCTCATTTCTTGGGGCTTGTCTGTTCCTTGGAACTGTTGCGCACGGT
TACACTGCCCCCTTCGAGAAGTATCCCGATTGCCAGGGTAGCATGAATAT
CAACTGAACTAAATTCCACTATGTCTGAAGTACAGTGTTCAAACTTTCAA
CAATGGTACATGAGTATAAGCTGAATTAACTAATCACATTCAGAATTCAA
GACAAAAGGTGAAAATGAAAGTTCACTGATGTACCTAGCTAAAGTTAGCG
ACTTTGTTCTTAGGTAAGACACATGTTTTGTGCTTTAATCGCTATTTGCT
AGACTGTTGGTTGCTGCAGAATTTGCTTGATTGCTTAAGAGTGCAGGGAC
ATGTAAAAATTGCATTGTGAATGTGTTTTTTAAAGGTTTGTTTGGTTGTT
CCCGTGGACACA
Sequence Length: 
7512
Sequence Checksum: 
0b564fc7dc9cf426a60e634b67a97ef3
View location in JBrowse: 
DCARv2_Chr6:17763336..17770847+
Gene: 
LOC108225774
Gene Biotype: 
protein_coding
Gbkey: 
Gene