LOC108214744

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108214744
Identifier: 
LOC108214744
Cross Reference: 
NCBI Gene
Relationship: 
There are 5 relationships.
Relationships
The mRNA, XM_017386909.1, is a part of gene, LOC108214744.
The genetic_marker, MK017672 3_38087594, is located in gene, LOC108214744.
The genetic_marker, MK009527 3_38087627, is located in gene, LOC108214744.
The genetic_marker, MK007607 TP135539, is located in gene, LOC108214744.
The genetic_marker, MK009525 3_38089625, is located in gene, LOC108214744.
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_017386909.1XM_017386909.1mRNADCARv2_Chr3:38087116..38094589
Sequence: 
GGACTTGGAGTAGGAGAAGGAAAGTATTGGGAAACGAAAAAGAGGAGGTG
GAGAGGGTTTGGTATAATTTTACATTTAACATCAGTTTTGTCTCTCTTCC
TCTCTGCTCCAGAGCGGCGATCGGATCCTTCTCCTGATCCGACCCAAATT
CAATTTTTGATTCACATTATCATAATCTTCAACTAGTTGCAATTGTGTTG
AAACACACAGTCGATCAACACAAGGAGGCTTAGCTTATCAATTAATCTAT
CATCTTAATTATCAAACCCTAATTTCAATGGCAGCTGCAGATACATCGTT
ATCCTCCTCATCATCCTCATCTGTATCGATGACTAGTCCGTCTTGGACTC
AACAAGAAGAAGCGCCGCCGGTGATTTCTGTTGTAATCGGCGGTGAGTCT
GGTAATCAGGATAACAGTAATGCTGGTGGCTTGAAGCAAGTGTGGGGGAA
GCCGGTTAATGTGAATGGGAGTAGTGGTGGTGCTGCTGTTTTGAGTGCTG
CGGTGGCTACGGTTGATGTTAGTTCTCGTGCTAGTGAGGCTCCTGCTGCC
GGTGTTGTTATGGATACGCACTCGTGGCCTGCGCTTTCCAAAGCGCCTCC
CAAATCTGCTTCTTCCGATTCCGTGCCGACATCTCACTCGGTTTGTTTTC
GACTCTTTTACTTGCGTAAAAAGTGTCTATATGACTCTTCATAATTGTTA
TTGTCGATGTTTATAAATGTTAATCTATTACTTACATTATGTGATACATT
GTTGAAGTTGTGATGGATTTTTTTTTATTGTAAAACTAACTATTAAGAAA
TAATCTTGAAAGCAATCTATAAATCAATTATAGATAATGTGTGATTAAGA
AGAGGATTGGGAGCAAAGAGGGTGAGATTAGTAGTATTATTATCATTACT
GACATTGGTTTTGATGCAGTGTTGTTTGGAGATGAGAGAAATCCATAGCG
TAGAAATGCATTTGCAGTGTCATACTAGAGATTAAAATCTCTTAAGACAT
CCTCAAGTTTCATCATTTTTATCTTCTGGTTAACATTCTTCTTACCTCCA
AAATCCACCCTCAAAATTGCCAGAAAATGCTTCAACTTTTAAATTTGCTA
ACAGTCACGTTCATTATATACCTTTGATTTTAGATTCTTTACGTATATAT
TAAAATATCTTACATGGCCCTGGGTGCTGATTCAAGTGTCAGATACTTAG
ATGGAATTTCAGGAATCTTAATAATGGGTCTGAAAGCTTAACCAGTAAAT
ATTCATATAAATTAATTTATCATACATTGATAAAAAGGCCTACTAAAATA
AATTGTTTACACTTTTACTTATGTTTGTTAGATTATTGCATCAAATCAAA
ACAATAACATATGAACAAGTCATATAAACAAGTTGTCGAGACCTTATTTA
CCATTTTGAACTGGGTTGCTGCAAGGTCATGTATCTGATTTTAATACGAA
GTACTCGACTCGGATCTCATATCCACACCCATGTCTTGTCTAGTGAACGG
GTATGAGGAATGAATTGGAGAGTCCTACGAGTTCTAAAAATTACCTTAAT
CTCAGGTTTTTAATCCTCTTAATACGTGTTATTTATATTTGTATTTATAA
TTGTTGCAAGTTTATTCCTTATAGTATTTTTTACTAAAAATTGTTGTTAT
ATACTCAAATTATAATCAAACATAAGGTATGTGATGTGATAACATATATA
AGCTAATGAATATTTGAATGAAATCTGATGAATTAAATATGTTTATATAC
TTAAATATTTGGATATTTTATCAGTTGGATATGCTGACATGTGAATGATT
CCATGTTTTAGGGTAGTGGAATGGGCTCTATATCTTCAAGTAAACAAGTT
ATAGGAAATACTTCAAGTCCTAATTCAAATGTGAATCATGTAACAAATAC
ACGCCAAAGGTCTATAAAGCGTGGTACAAACAATGGTGGCTTTATTCAGC
CATCTTCACCACAACCACAAGCTCCAGCTGTGGAAGTGCTGCCAGGAAAG
CCTGGTATTACTACTGGGGAATCTTCCTCCCATAAGGAGGGTGGTCCAAA
GGGAGGATTTGGGAATGATCACCAACCCCAGCGTAGTAATTCCTTTAACA
GGCGGGGAGGTGGTGGGCAGCATCCGCGTGGAGATGCTTCTTATCATCAT
AGTTCTGGGGGAAGACGTGATCAGGATCGTGGGAATCAGGACTGGAATCA
TACTCAGCAGAGTTATGGTAGCAGAGACAACTACATGCAGCAGCAGAGAG
GTGCTCATAGGGGCTATCCACGAGGCCCGCATGCGTCTCCATTCATTGCT
CCTCAACCTTTGCCTGTCCGCCCATATCCTAATCACATGGTTTTCCCCAC
AGGTGAAATGTTTTGTCATTAATTACATAATAACTTGTATTTCTGCTCTA
TTTTATTGCTTCCTAACCAACATTTAATATGATAGCAGATGTTCCGCAGC
CTGTATTTTATGTTCAAAGTCCGGAATCTCTTAGAGGAGTTGTGCCTATC
ATGCCACAAGTGGCAGCTCATCCTATGTATTATCCTCCCATTCCAGATCC
TCAATTGCATGTTAAGATTATGAATCAGATAGAATATTATTTCAGGTGCT
TCGTCATCGTCTTTGTTTACTTTATATTGTGTCTGGTAGTTTTGTTGGGA
ACCCAGTAACTATTCATCTAACACTTTTGCTTTTGCAGCAATGAGAATTT
AGTTAAAGATACATTCTTGCGACGGAACATGGATGAGCAGGGATGGGTTC
CTATTAAGTTAATTGCAGGTTTTAAAAAAGTGAGTTGTTATGAATGCGTG
CGCGCGTGTGTGTGTGTGTGTGTGTGTGTATGCAGTTATGCTTATGCAGT
TATGCTTATGCAGTTATGCTTATGCCTCTTTCATATTAAATTTTCTGTTT
AATTTTATTGAAGTTCTTATTTATTTTTGTATGCGTTACTTTATCATCCA
TTATTCTCTCTGTTGGACAACATCAGTTCTAGTTGTGGACTTATGATAGT
CCTCGGAAAAATTATGCAACTCCATGAAGTCCTGCACCTTACATGTTGTG
ATGAACTTGTGGAATTGTTAGATTTCTTAGAAATTTTCTCGTATAGGAGA
TTAACTTGCTATGAAATTTGTGCTGTACTTGTTTCATGTTGTAGCTAAAT
ATATTCTTCTGCCTAATTTAATTGTCTTTTGATCATCAATAACTTAAGAT
TATAGTAGATTAGTAGTAAAGCTAATTAAAGGTATAGTGTACAGAGTTAT
GTTTTATCTTCATGTATAAGTCTATTATTTATTGGACAGGGGGTTAGAAA
TGGATTGTCAATGAATATGGACTCACGTCGACCTTGTTAGATACTCTTTG
AGATCTGATTGGCATGATCCATTTAGTAAATGGATTAGATATGGATCACC
CATGATTTGATCCAGTATAGACCTGATGTGTTCCTTCTGTACTTGTGGCC
TCTTCAGTCTGTTGCATCATACATTCTGATTCTTTGGCAATCCCTCTCTT
ACATTTCAGCTCATCTTAAACAGTGAGCTGCTGATGAAATCTCAGTGGGT
CCTCGATCTTTAATTTCTTCATTCTTAGAACAGGTAATTTTTCTCCTATT
GCTCATGGAGCTTGTTCTTGTCTCGAGGGTCGAGGCCCTAACCAGCTTTA
CTTAGGTTTTATCTAGTAAGAGTGATAGTTTTAATAGCTATATCTTGTGA
AGGTGATCTTTTTCGATATTTATTCTGAGTTTTGATGACTCTGGAAGGAC
AAAGATTGTTATGTTTATAGGAGGTCTTTTATACTTGAGTTGGAATGTGT
TTTTTCTCGATTCTTTAGTAAACACCCATTTTGAATTCCAAAAGAGTCGG
ATTCTGATTAGTTTGTAAAATATTAGGCAGCTGAGCCGATTCTCCTAAAA
AAATTGTTATACCTGTATTTGCATCAGCTGCGGTCCGACTCGATGCCGAT
CTGTTTACCACCCAAATTGGTGTAATCTAAGTTACCTGGACTTGGGTATG
GGTGTTGGACACGGGTGCAGATCCAAGTGTCAGACCCTTAATTTCTTAAA
AATTAAGATTCATGGATATGGATGTAAAATTGGACACGGGTACGGGGATT
CGGCATATAACCTTTACAGATGTGATATTATTTTTGTACCTACATTTTAT
ATATTATAAATTTGTAAATAGAGTCTTTTACTACTACAAAGACATATACT
AATTGTTTATTTTATACTTATAGCATAAATCAAAAGTAGCATGGAAATTA
ATTTATAGGCGTCCCTCCCTAAAAACAAGTTCGCAGGCTTTATAAATCAT
TTTGAACGATATTGCTTGAATTCGAAGTGTCTAGTTCTCAATTGAAGGAT
CCGACACTGATCCCATACCCACACCCAGGTCATGGCTGATCGACACGGGT
ATGAGGGCAAAATTAATGAGTCCGGGTAACATAGGGTGTAATGTGTCATA
ACTACAAAAGTTTATTGAATTTTGTATCGTTGTTTATTTCCAACTGGTCT
TGAAGTGTACTTTAGAATGAAGTACAACCTGTGTGTTCTAAATGTAGTTT
TGTCAAAAAAACAATGTCATAAATCACTAGGATACTATATTTTATTATAT
TCTCTAGGGAATGCACTAGGACACTATTAGACTTACTGTTAGATGTCATT
AGTCTTCACGTAGCCTCTAAGATATTTGGTAACATCTTCTTACCGTCTTC
TAGAAGATATCAGTGCACTGTTAAAGCCTTGCTACCAATTTTCTTGCCTA
CATTAATAGTTTCATACTGATCTTAATGTAATGGCAGTTTCTTGTACTTA
GTAGGGTGTGGTTTTCCCAAATTGCTACTCCCTCTGTCCCAACCATTTCC
TTACAATTTCCTTTTTGAGATGTCCCGTCCAATTCTTTACATTTCAAAAC
TTACCAAATATAGTATAATTTTATAATATTAAATTTAACCATCCCCACTA
CTTTTCTCCACTATATTTACTTTATACATTAAATATCGATCGTTCGTATC
ACTATCATCACTTTTCTTACATTTTCACTCTTACTTCACATATTTTATTA
ACCTCCATGCCCAACCCAAATGTGAACATTTGGGTGGGACGGAGGCAGTA
TATCATTATGAATTTTCTTATTGGTTATGGTCTTCATATTAATAGGTAAT
ATCTTGCATGAATAGTTAATAGTATACCCTGACAATTTAGTTACAAAAAA
AAAACTCTGTTATGTCCTGCAGTAATGACAAATTCACGCAACATTTGCTC
CTTATTAGATTCTCCATCACCGAATGTTGTTAATAGTTAATTTTTAGAAT
GATTAATTTGAAATTTAGGTACGTTATACATCTCATTTTTAAATTCTTTT
GAAAATTGAACTTTCAGTGCGAATATATTATTTCTTTTCTGACTTGCACG
ACTTCAATGGTAGTATCTACCATTCAGTCAATATCCATTCTCATTCAGCT
CTGGGTATTATTCTTATTCTATTTTTATGATATAAAACCCCCTGAAGTAC
CTTTCGATGTAGTCAGCGACCTGTAGCAAAGAGATGAAACATTCTTTATC
AAGTAGGAAAGTCAGTGGTATCCATAAGCTTATTTATATTCATCTTTCTA
TAGTTTCTTCACTGAGCTAAAGATGATAATGTGTCCTAGTTTATGTTAAA
ACATGTCAGAGTTTAGAGGAACAATTTTGGTCCGAATCGAGTGAGAATGA
TGATGAAACTTTAAATGAAGAGGGACAATCAAAGCATAGCAATCTGAATG
GGATCAGCTTGTTTTTGTTTGTTTCCTTTTCTATTCAGAACTTTAGGCGC
ACGTTGACATAAAACTGATCTAAGCATATCTGTTGTGCTGAAGTGAAGGC
CTTCGCTACTGACGGTAGATTCACCTATATCTGCCGATTCTCTATCTATT
CTTCTATTAGTTGATGAACTTTAATGCCAAACATATAAAACTCTGTATTA
TATTTGTTTGCTCATTTATTGAAGGTTTATTAGCTATCAAAAACCTCCAG
GGGAGCTCAGTAGTGCATCAGATGGTGTCTAGAAAACTAGTAATCTGGTA
GGAGAAATATGTGATACTTTGCACTTACGGCACCATTTTTATCTCTTGCA
GGTTATGAATTTGACAGACAATATTCTACTCATATTGAATGCTGTTCAGG
CATCGACTGTTGTTGAAGTCCAGGTATTTATTAATTCACAACTTGAAAAA
AAAACCCTCTACAGTTGATGAATGATTGAAAATCATTTGGATTGGAGTCA
TTGGACAACACAGAGATCATTTTTTGTATTGCTGACGTTAATCACTTGAG
GCTTCTTTATAGGGTTTAGGTGCTTTCCGTATCATGTTTTTTCCTGATAT
GTAGAACCCCTCCCCCTCTCACCATAGCCACTCACAGGCAAACACACAAC
TGAAGTACTAAACTCCCCACCTGTTATTTTGAGTTTTCAGGTTAAACATT
ATATATAAATTTTTGCTTCAATGTTATTTATAATAGGCATTTATGTTCAA
TTGTTCAGAATGACAGAATTAGGAAGCGAAATGAGTGGATGAAATGGATC
ATGCCTCCTGGCCCGTTTTCTCCTGTATCAAGCCCCCAGGCTCGTGCAAA
ATCTGGTCATGATATGCTAACAGGTCAGTTTCAAGGTGTTACTTTGGATG
AGAGGTCGGTGCATGGCCACACTGACATGTTTAAGAAGTCATTATCTGGA
GAATTTAGTAGCCAATTGCAACATTCTGGAGGTGAAGGTGATGTTCATTC
TGGTTTTGAGCACAAAAGTTCTGCGGGGAGTCTAAGTAAGTGATCACAGA
TATTTTTCATGCCTAGTCTGAGAGAGAAAGAGAGGGAGTACTTCTATGCC
GGTGACAAACATTTTAAGTCTGCTGGGTTGTCTATGTATCTTACCAGTTG
GTGATGGTTCTGCGTCGTGGAGTGGGAAATAGACAAAAAAAATAATAGGG
GAAGAAAAACATAAAGAAGAAACGTAATAAAACTCTAATAAAACAACAAA
AAACGAAGAATATGTTGCGACTTGAAGGAAGTGTTTGAGAATTTTGGATT
AATGTTTCATAATGGTTGGGATCAGTTTTATATATTTATATGTGTTATGA
TTTTGTGGTTTGCTTGTGTATCTTATTGGGGAATTTTGTTCCTACTTCCC
CTGAGCTTACTACCCCTCAGCCAGTTTTTGAAAATCTTTGGGGTCTTGAT
ATCTTCCATTGTGGAAGTAAGATGAGTAGCTTCTTGAAGGCCATTGGTGT
GTTTTAGCAGATGAAAGCCATAAAGCTCTTGTGGTGAATCGGACTCAATG
TGGCTTCATGCACTAGTACTAGTGCATGAATATATGATCTGTGATTTGAT
CTATGTACTATGTGCTTTTGTTGAATTTTATAATTAAATTCAGATATATA
CATTCATCATCTGTTAAATTTATTGCAAATTTGATTTGCACAAGTGAGGG
AGTGTCCTGGGCTTTGTTGTGCC
Sequence Length: 
7473
Sequence Checksum: 
6d2f3891be884d5bb680686d988e5029
View location in JBrowse: 
DCARv2_Chr3:38087117..38094589+
Gene: 
LOC108214744
Gene Biotype: 
protein_coding
Gbkey: 
Gene