LOC108200102

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108200102
Identifier: 
LOC108200102
Cross Reference: 
NCBI Gene
Relationship: 
There are 4 relationships.
Relationships
The mRNA, XM_017368169.1, is a part of gene, LOC108200102.
The genetic_marker, MK001043 GSSR-044, is located in gene, LOC108200102.
The mRNA, XM_017368170.1, is a part of gene, LOC108200102.
The mRNA, XM_017368168.1, is a part of gene, LOC108200102.
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_017368168.1XM_017368168.1mRNADCARv2_Chr8:25923708..25931155
XM_017368170.1XM_017368170.1mRNADCARv2_Chr8:25923708..25931154
XM_017368169.1XM_017368169.1mRNADCARv2_Chr8:25923708..25930945
Sequence: 
AGATTGTGAGGTGAGGGCGCGTTTGTGACACGTATGTCCCCTCGGCGCCA
CGTGTGAAATCCAACCCCAACCGTCGTGCTCATCGTACCTTGACTTTTCA
TCTGCAGCACACTGTTAATAGGAGTAATTCACAGATACCCCTTTCTCTTC
CCTCAACTTCACCCCAGCTCGCCAGGTTCTCTCTCTCTCTCTCGCTAAGT
ATCTTATGACAAATCTCTCTCTCTCAATATTCAAGTACCTTCTGACAAAT
CTCTCTCTTCACACGCTCTCTCCCTCCCTCCCTCTCTCTCTCTCTCTCTC
TCTCTCGCCCCCTCCCTCTTTCTCCACACACACACAGTAGTTTATGTGAT
ATGTATGTTTATGTATCTATGCGCTGTTTCTTTACTTGCTTTGACTAATT
TCCCATTATTTTCATCGTCCAATTATGATTCTCTGCTACATAAAGATCAT
ATCTTTGATTCGAATCACTTCAATTTTATTTTAACAATCATTCTATTTTA
TTCATGTGTTCAAGGGGTGCTTTGCACACTTGTTGTTTACAAAGATAATT
AATTACTAAACTGCTACTGCCCCGAAAGTTTTTTATTTTTTAAGAATTCT
TTTTCTAGTAATGTCCATTTGTGGGGTTGAATTGAAAATTTGGTAATCGT
AGGCACATTTGTTTGACGGATTCGTAGTTTGATAATGTTTTGTTTAGTTT
TGGTCGTTGCTCATGGTTTTTGAATTTGTGTGAATGTGCACTGCTTGTGT
TTCAGGACCGGCATACCTGCTCAAGGGTTTGGGCATTCTGCTAGTTGAAT
TATCGATTTTGTGAATGTAAAAAAATGAGTAGGACAAGAAACTTTTTGGT
CGAATGCGGGTCTGCTACTCCAAGTGAACCATATAACAGTCACGATGAGC
TGTTGGGTCTTGATCATGACATTGCACAGCTTACGAGGCTTAAGTCAGAA
CCTCACAAGTATATGAGTCGAAGATTACCGGGAAAGTCGATGTTGCCTAT
CTCCCCTGTGGAAATGCTAGCGCGCCGGGAGGCTAACTTTTCTGGTCGTG
GCAGGTTTTCATCTGCAGATGGCTGTCATGTTTTGAACAGATACCTGCCA
GTCAATGGGCCCTCTTTGATTGATACAATGGACAGCTCTGGTTATGTATC
TCAGTTCTCTGGTGATGGATCTCTTTTTGTGGCGGGATTTCAGGTATCTT
TTGAGGCATGGTTTTCATTTTGTAAAGATTAAAACTTGATGTGGATTAAG
TTTGGATAAGCCTTTTACTCCCGTTCTCCTCAGGAAAGTCACATTAGGAT
CTATAATGTTGATAGTGGATGGAAAGTTCAGAAGGACATTCGTGCCAGAA
GCTTGAGATGGACAATTACTGACGCATCTCTTTCACCTGATCAACGTTTC
CTTGTGAGTTTATAACCATGATTAGACAATAGTTAATATGCTATGCACCA
AAATGCTGACTTAGTTTCTTTACTGTTTTTTTACTTTATTGTTAATGCCC
TCAATTTGTTGATGATGTATTGGGTTCCCTGTATCTGCTTTTACATGTTG
CTTGACTGAATTTTTATAAATGCTAGTTCACTTTAAGGCTTTGAGCTCGC
CCTTAGTTTGAACATTCGTAGAAGGTTAAACCATAGCAAAGTAAAAATTT
ATTATTATTTCATTCTTTTGCTGGAAAGTGGAATCTAAAGCATATAGCAT
TTGACTCGGCCATAAAATGCTTTATATATCTTCTGGAGTTATATGCCTAA
GCAGTTTTTAGGAATGTTTTTGGCTCCCATGACTTGATTATATTGACAAT
ATGCCTTGCTGACCTTCTAATAGCAGTGTCTGTCTTTTAGCCCCTGCTGG
AGTAGGTTCAAGTGTAGTTCTGTTAAAGTTTGTAGAGATTTATAAATTAC
ATTACAAAGGATATCACATAACTACTTCTTTGCACTGTCTCTCTTAATTC
TGGAAATTCCCTTTCGAGTTTCGATCATGTAACCACTTGCACAGATTTAT
CTTAAAAATTTGTGCCCTACATCAAGTTTTGTTATGTCATTCAATCAAGT
AGGCAGTTTTTAGTGCCGTGATGTGTTTTTACATACTATTGTGGCCAAGT
CTTTAAAATTTTAGGTTCTCCCTTTGTACATTAACTGCAGTCCTTTGAGA
AAGACCCAAGGACTTAATTATCAATTTAGGTTAAAAATATAACAGAACAA
TCTCTACACTAGATAATTAGTGAAAGAAATCCGATTTTCTGTTTGATTGT
GCCGGCCAGCTGCAATGATGAATAAAGCCAACAACTTTGCTTCGCTACAT
ACTCACTTTTGTTGGAGGCCTATCTAATATTGTGCTGATGATATTTTCCA
TATCAGCTAGTAGTGGCTTAAGACATATACTTAAATGATATGCTAACTCT
TGCCGTTTATGAAAATTATATTTATAGTTGGTCATATGCCTAATTATGGG
CTTCTCCTTGTTAGTTAATTTACACACGTTCTCACGCCTAAAGTAACATG
TCTCATATTTAACATCTAAAAGTGCAATTCTATGCTTAAAGACAGTGACA
AGGCTATACACACTCTAATACAAGGATTCATGGTTTCCTTTTGTTTGACC
CCTCATTAATATTTCTTTACCCACAATCGAAGTTGAATGTCTATAGCGGA
AAATTCTGAGAAATTTTTGTTATATTGCAGGTTTATTCCAGCATGTCCCC
CATTGTTCATATTGTTAACATTGGATCTGCAGCAACAGAGTCTGTTGCAA
ATATTACAGTAAGTCCTGAAAGTTCATCCTTAGATTTAATATAGAATAAT
ACAATGTCCATATTTATCTGTTTTAAGGTATAATGTGTTTAAGAAACATT
TTCATCATCGAAGCTCTGTTATGCAGGAAATTCACGAGGGTCTTGATTTT
TCTGCTGGTTATGACTTTGAAGATGACGATTATTATTACGATGCTTTTGG
AATATTCTCTGTAAAATTTTCAAATGATGGACGAGAACTTGTGGCAGCAA
GTAGTGATGCTTCAATATATATCTATGATCTTGGTGCCAATAAGCTTTCC
ATGCGGTTCCCTGCTCACATGGTATTATAATTCCTGTTAGTATTTTTTGT
GAGAACTGTCTGAATTTATGAATAATTATGTTTTATTGTTAATTTCAAAA
AAAATTATGTTTTATTGTTATCTGCAAGTTTCACACGAAAGCGAGTTAAC
CTATCCTGTAGCTGTCCTAATCCTTACAAATCCTATCCTGTTCGCAGATT
TAAGTTACCTAATCATTTTGAAATGTAATTAGGCGATTTATTTCCTGTGC
TGTTGTGAATAGGTTTCTGACTTTCTTCATTGTGGTAATCTCAAACATAC
TTATTTAGTATGAGGGATCTGTACATTTTCTAGATGCAAATCACTTGATG
CAGATTTTATGTGGTATATTGGGACCCTAGTCACGTATAGGGGTGTGTAT
CGGGTGATTTGGTTGGGTTTGGACCGTATAACTAAACCCTAACTTTTAGG
TTTTTGATTTTTTAAACCAGAACCAAATCCAAAACCATATACATTCAAAC
CAAACCAACCTGAATCAAAACGGTTTCGGTTCAAAACAGTTGCTAAGGCT
ATTTTATGTTTACTTCCTCAAAAATACAAGGTTCAATTAGTAAAATGAAA
CAAAATTAATTGGCAACAAAAATCGTAGCATTAAATTAGTAGCACCAATA
ACTTTTGACAGGTTTGTGACCTGAAATGAAAATATAAAATTATAATATTA
TTCCTAGTAGCAGCCAGGTACGCGGTTGTCCATAATGTTTTCCTGGTTTC
CTTGATCATTTTTAATTGAACAAATTGCTTTGATTTGTTATTCTATATAT
TTAGGCTCTATACTCTTCTGCTATACTGTAAAATAAATTATTTAATGCTT
ATGCTTTTGCCTTGGATTAATAAATCAGTCTCATTCTTTGATTGTAAAGT
TTGAAAAACTATATATTATATAAACATTTTCAAGAAATTGGACCGAGATT
ACTAGGCCACTGTAATTATGCTTTGTTCTGTGAACAGGGATTAGTTTTTT
CATGATTCGGACGTGTCATTTTGCATTCCCAATCATGATGCGGATTATGA
TCCCCTCCCATTGTTGTTATAGATTGTAGAGATGGCAATCGGGTTGAATC
GGATATGGCACTATCCAAAATCAAACCTGGATTTTTTATCCATGCTCAAA
CCCAAGTTGAATCCAAAAAATACCCGAAAATGAGAACCTGAACCCGATTC
TACGGATTTCGGATCGGATTTGGGTATACCCGAAACCCGATCTTTTTCAA
GATTGGATATGGATATACCCAAAATCTGAAACCCGGACCCGAAATTTGTG
GACTCCATAGAATTTAACGCCTTTTGGCTTGAGCTGGTAGAGAATATTTG
TGTTTGTGTTTACAGTTTGGACAAATTATGTAGGTCATCATTGGAGATGC
CCCCTCACTTGGTGAATCATGTTGGATTGAGTGAACCACATAATTCCTTA
TTTGGTGTGATTACTTGATAGCTACCTTTCACTCAGTTTGCCACTTTTTC
TACTCTGTCAAAAACAGTAATGTAAATCTGACACTTAATTGATGACTTAT
TTGCATTTTCTGCTCCAGTGTGATGTGAACACAGTGTGCTTTGCTGATGA
AAGTGGTCATATCATATATTCTGGGAGTGATGATGGACTGTGTAAGGTAA
ACATTTTATTTCTTTATTTTCTGCCAAAAGTAGTTGTTGGCATTGAACTG
CCTAAGACTTGCTTCCTGCATATACTGCCTCTTAGCATTTGTGAATCAAA
TTAGCACAGGCTCCCATCAAAATTTTGTTTTTTGTTTCAAATTGCCAGAC
CATCTTATAAGGGGTGCTTAAAGTTTTGGTAGTCTGTCATGAGTCATGAT
TATCATAAATACTGATGATTGAGAATTATAATGCTTAATTTTCTATCTTA
TACAGGTTTTGGACAGACGTTGTCTCATTAATAACGAACAAGCATCTGGG
GTTTTAGTTGGCCATCTAGAAGGTGTAACATTTATTGATAGTCGAGGTGA
TGGCCGTTATCTTATCTCAAATGGAAAAGATCAGACTATTAAACTATGGG
ATATCCGGAAGATGTCCTCTAATCTTTCTCAGTATGTCTTCTATCTTTCT
TCTACCCCATTGCACATGTTTGACTTTTTGTTTAAGGATTTACTATTTAA
GAGCTCATATACTTTTTATGGCATCTCTGCTGGCCTAGCTGTTTGTGCTG
TCAGCTCACTAAATTGTCAATTAAATTTTGAATTGTCAATCAAGTTTTAA
ATGAAGGTTCACAAGATGAATTATTAGCTACCACTTGTCAATTGAATTTA
AGAGATTTGTCGCCTTGTAAGATCTGAACGTGGTCTGTGCCTCTCTCCCT
ACAAATTTTATATTATCAATCTCATTAGTTTCTTATGCAGTAATCCATAT
AAAAGAAACGTAAGATGGGACTACAGATGGATGGAGTACCCAGTTCGTCT
AAGAAATTCTCGTCATCCGAATGATATTTCTTTGGCGACATATAAAGGTC
ATTCAGTTTTGCGTACCCTCATACGGTGTTACTTCTCACCAGCATACAGG
TGAGATTGAAGTGATTTACCCTGTGTATGTTTTCAAGTTATTTTCTGCAA
CCTACTTACTTAATAACATAATAACATGATATTTCTATAGAACTGTTATT
TAGCCTATTTAGTCGGTGAACATTCTTGATTGTTACTGTAGTTTTTCATG
AGAGTTTGACTTGGCACCATTTGGTTCTGCAGTCAAGCTTTTCTTGTTGA
TCTGGATTTACCTAGTCTATTGTCCCATATGCTATTAATTGCATCTACTC
TCTATGCTAATTAGCTGAACTTCTAGTATTACTAGTACTTTCCTAATTTT
AGGATTTTATTAATCGGATTAATTACCCTAGTTTTCAAGTGCTAGTCGAA
CTTCTAGTATTACTAGTACTTTTCCTAATTTTAGTATTTTATTAATCAGA
ATAATTACCCTAGTTTTCAAGTGCTGATAGTGGTATTAACAGCGTCCATT
TTCATGGATTACTCTTTATATGAATCAGAAAATTTAAAAGGGTAGGAGGT
ACAAAAAAAATACTGTATGGCCGGAAAACCTTAACTTCCCTCACTTCTGA
GCCCCCCACCTCTTTTGAATGAAATAGAATCTCCTTGGTGAAGAAACCCT
GCCTAATAGTAGCTGACTTGATGAACGATCTTGTTGAGTTAAACTCATCC
ATCTAAGAAATCCCTTTTGCCTTTTACTTTGAGGCCAGTCCTATTCCTGT
AGGGTAAAATTTTTAATATCGACGCTAAAAATGTCAACAGACAAACAATT
ACTGACACATTATATGTGCTGGAAACTAGACTTTTACTGATTTCCTGCAT
ATTGGTTCTGTTATAGCTTTTGCCAGTAGTCTAGTCTATTCGTCATATTG
CAGCAGATGTGCTGCCTTTAAGATATTCTTGGATCTTTTATGATGACAAC
TTTCTAGCATCAAAGGATTCTCTCTGCTAATGAATTACTTGTGTAGTTAC
CTGCATTTTTTACTTGGTGCAGCACTGGTCAGAAGTACATTTACACCGGA
TCTGCTGATGATTCAGTATATATATATGATCTGGTAAGCTTTCAGTTTGG
TAACTCTTACGCTCCTGCATTGCAATTTATACTTATTTGTCATCAAGAGC
CATTCAATGTAGAAAGCCATCCTTTTGTGCATTTTGTTCATACATGTAAA
AAGGCAAATCAGGATAAGATTTTCTTAATCACGTGATGGTCCAAACTTTT
GAGGTCGATGTAAAGTATTAAATTTAAGGGACGTGTTGGCTATATAGTCC
CCATGGTCTTGTGTAGCTGAGCTGTCCACCTTGTAAACTGGTAACATTTG
TATATCAATATAACAACGATACCCTTGACAGTAGTTTATAGTGAAATCTA
CTCAACGCAATGTGTTCATGTTATCTCGTTTGCTTTAATGGTGCTCAAAT
TTGATATATCGCCGTAATTGGTTGCAGTTAACTGGAGCTCAGGTTGCCAA
ACTCGATTATCATGAAGGTCCTGTAAGAGATTGTAGCTGGCACCCGAACT
ACCCTACTCTAGTTAGCTCTTCATGGGATGGAACTGTTGCAAAATGGGAC
TTCTCTGATAAATCTTTAAACCAATCCTCTGAGACTGAGACAGTCTAGTC
AAATTTGGTGGAGCGTCTACTAAATTGTCAGCTATCCAGCAATATTGACA
TGTTCTGTAAATTATGTCTAGTCTAAAATTCTAGAGCTCTGTCTCTAGAC
TGTGTTTAAATTATCGAAATAAATATTTTTCTTATATTGTAATTAACGAC
TAGAAAAAAGATGGTGCAGTTTTTACCTTATAATCCCCCGAGTCATATAA
CATTACACACAGAATACATGAATACAAGCCAGTTTTATCACCAACAA
Sequence Length: 
7447
Sequence Checksum: 
1a490327e21d679081d3aa9c499952fb
View location in JBrowse: 
DCARv2_Chr8:25923709..25931155-
Gene: 
LOC108200102
Gene Biotype: 
protein_coding
Gbkey: 
Gene