LOC108196248

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108196248
Identifier: 
LOC108196248
Cross Reference: 
NCBI Gene
Relationship: 
There are 8 relationships.
Relationships
The mRNA, XM_017363448.1, is a part of gene, LOC108196248.
The genetic_marker, MK008360 7_122881, is located in gene, LOC108196248.
The genetic_marker, MK008855 85036.37499, is located in gene, LOC108196248.
The genetic_marker, MK018710 7_123400, is located in gene, LOC108196248.
The mRNA, XM_017363447.1, is a part of gene, LOC108196248.
The mRNA, XM_017363443.1, is a part of gene, LOC108196248.
The mRNA, XM_017363446.1, is a part of gene, LOC108196248.
The mRNA, XM_017363444.1, is a part of gene, LOC108196248.
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_017363444.1XM_017363444.1mRNADCARv2_Chr7:114779..123641
XM_017363446.1XM_017363446.1mRNADCARv2_Chr7:114779..123535
XM_017363443.1XM_017363443.1mRNADCARv2_Chr7:114779..123535
XM_017363447.1XM_017363447.1mRNADCARv2_Chr7:114779..123534
XM_017363448.1XM_017363448.1mRNADCARv2_Chr7:114779..122332
Sequence: 
TATTATAGATAACAATATATATGGATTAGAAAATTTTGGCCAGAAGGGGT
AGTACGGGAAATTACGATGAAAGGCTCAAGTGAAGTCCAGCTTTATTGGG
TATGATCACAGTTTCATGTCTTGCAAGAAACACCATTTTTAATTGTTTCA
AGAATCAGTATATATATATTTATACCTGTACATATATCATCATTTGAAGC
TGCACAGGTACGCTTTTATGTTGTAGTTGCATGCTTGATGAGCCTGCTGA
GTATTACAACTAAGTTTCAGCTGCCTAGGATATATTTCGTTAGTTCAAAC
TTTTAGCTAATATTTGCACCTTACGTTTCTGTTTGAGTCTGCAATTTTCG
ACATTCAGTTACAGGACAATGAAATTTAATTCTGGTACAAGTGTTTCGGT
TCGGTCCAGATAAATAATTGATGCTCCATAGTACTAGCGTTTTTTTTCCG
TTAAATCGGGCTACTATGTCTCCAACGAGAAAAAATTGTTAATCCTGATT
TGTAAATTGTTTGATCTGAACCAAGATTCCTGTGTGTTTATTGGATGCAA
GAATGGAAAGAATACTAAACTCTTCCATGACTAATTATATATCATAAAAA
GGTAATAAAATTAATGCATAACACACACAAAAATATTGATCGCGCCTAAG
TAGATTAGATTTTGTACACAAATATGTTAAGTGTGATTTTATTTTAATTT
TTTGGAATCTGCAGTGAAGTGAAGTGAATGTCTTCATCTTATGGCAGCAG
TATGCTTTCGAGGTGTATTAGAAATACAGGGGATGTGTATACACAAAGAT
TGTTCAAGGAAAAGTATGCAGACCAGCAGATTGATAGTGTTGGACCTTTA
CCTATTCCCGTGGGGCAGAGGACGAGTCGAGTTCGACTCAGTTGCTGCCA
CTCGCCAAATAGTCGTGAGACTCCAGCTCGGGGTCCAAACCGGTCTCAAG
CTATTCTTACTCCAATATCAGACCCTGCCAAGGTTTCCAAAAAGGTACAT
TTCATAGCACACTTGTAATTCTTCCCTGAATTGGAATTTTACTCTGCTAA
ATAAAATTCAACAATATGAAATTATTTGATCTGGCTTTGTGCAATTTTTG
TGACGAAAGAAAAAAGGATCAGTGATTGAACTAGATAAGATTGCATCAGG
ATCAGGTATCATCAATTCCAATGTAAAAGGTTGTTACAGCCTATAGGGGA
TGGGAATGGTTTTGACACAAGTACATACGTCGGCTGTTGCAGTTATCTAC
TTATCATCTTAATACTCTAAATTTGTCCTATTACTGTATCTTCACCATGC
ATGCATCTTTTTGTCTGTAATCACTATATAAGAACTAGCAATCTTTTCAT
TTTACTCATCAACCAAAATCTTGAAAGCTTTTTGCTGTTAGGAACCATGA
AGGTAATATTTAGTTTAGCTCACTGATGTAAAAAGAACTCGTACAAATGG
CTTTCTTTAACTGGAGATGCTTAGATATAAGTCTGTGCTTTCTCTGTTTT
CGTGCAGAGAGTATTCACATTTGGGAAAGGAAATTGTGATGGCAACAAGG
CTATGAAGTCTTTGGTAAGTATTGTCAGCTCATCATTCCACTATAATAAC
TTGTTAGGATCTTCTAAAATGTAAGGAACATAGCTTAATATGTAACATGC
TGTTTAGTATGTCCCTTGCTCGAGCCCATTTTTGTGATCGAAGAATGCAT
TGCTATAAGCCCATTGAGTGATTGAGACCACAATTAAAATCTGTGATTTC
TTATTAAGTTATTATGTCTTAGGAAATCTAAATGTCTTCTCATGCTTATG
ACTTAATTCTCTGAGTTAATTCACCTTTGTTTAACTGATCTTCATTTTTA
AGCTTGAAACTGTATTTTGAATTATACATTCCTCAGTGGTGGCACATTTC
TTTCAGTTGCTGTCTATGATTATATGTCAGTGTGAAACGTCTTTTATGGA
TGAAATTTTTTGTATTTGTACCATATATGTGTATTTAGCTTGGAGGCAAA
GGAGCAAATCTGGCTGAAATGGCAAGCATTGGTTTGTCAGTCCCTCCAGG
CTTCACTATTTCCACCGAAGCATGCCAGGAATATCAAAAAAATGGAAAGA
GTCTGCCACAAGGACTATGGGAAGAGATACTGGAAGGACTGGAGTTCGTG
CAGGAAGACATGGGTGCATTCCTTGGTGATTCATCTAAGCCTCTTCTCCT
TTCTGTTCGATCTGGTGCCGCAGTACGTATCTATTACTGACAGTGATAAT
TACTTAATTAACTTTAGAAAAATTCCTAGTTGCTGGATAGGTTTGCATGA
CCGGGAATATTTTGACTATCTTAATGAACTCAGAAGATTATGTTGCTTTG
TCTGTATTACTTGCTTGTATCAGCTGCTTTTTTTACCACTTGCTATTATT
CTCACTTTTAGATATCGATGCCTGGTATGATGGACACTGTCCTGAATCTA
GGACTCAACGATGACGTAGTTGCTGGCTTGGCTTCCAAAAGTGGAGAGCG
CTTTGCGTATGATTCATATAGGCGTTTTCTTGACATGTTTGGAAATGTTG
TATGTAGTTTCCTCTTACTTCTAAACACTTTAGGTTTCTGTTTCCTTTTG
GATTTGGCCAAACGACATGAAGTTTTTAAATTGCTTTTACTGTAATCTAT
TATCTGGATTTATTTGTTTTAAAGTTGTTCACAAATTTCTGTTTCTTGGA
AGGTGATGGGAATTCCACACTCCTCTTTCGAGGAAGAACTAGAAAATTTA
AAAGCTGTGAAAGGGGTTAAGGAAGACACTGATCTAACTGCTGCTGATCT
TCAAGAACTTGTGGAGCAGTACAAGAAGGTCTACATCAAAGCTACTGGTG
GAAAGTTTCCTTCAGGTATCAAGTATGGTCACCAACTCATTATGTTCACT
AGATCAAGAGAAAATAGCTTCTGATTTCTGTTCTGCTTGCTTGTCTTCCT
GTGCAGATCCAAAGAAACAGATGCAGTTGGCCATAAATGCAGTTTTTGAC
TCCTGGGACAGTCCAAGGGCCAACAAGTACAGAAGCATCAATCAGATAAC
TGGATTAAAGGGAACGGCTGTGAATATTCAAACTATGGTGTTTGGGAACA
TGGGGAACACATCCGGTACAGGTGTCCTCTTCACAAGAAACCCAAGTACA
GGTGAAAAGAAGCTCTATGGGGAGTTTCTAATCAATGCTCAGGTCTGAAA
GTGCTACATTCACTATGACTTTTTATCATAGATAATTATGAAGGCTTACT
TATAATGCTTCTATTACTTGGCTGATAAGCATCTTTCAACAGGGAGAGGA
TGTGGTTGCTGGAATTAGAACACCAGAAGACCTGAACACCATGAAAAATT
GCATGCCTGATGCTTACAAGGAGCTCGTGGAGAATTGTGAAATCTTAGAG
CGACACTATAAAGATATGATGGTAAATTTGTAACAGTTTGAAGTCATATT
GCTTGGCATACTTTTTCAGTATCTTAGCTGATAATATATTAAATTCAAAA
GATGTCGTTCTTACATATGCAGAATTACTGTAACTGTAAAAATATAAAAT
GCTTCTTTGTTGATTACAGGACATAGAATTCACTGTTCAAGAAAATAGGT
TGTGGATGCTGCAATGTCGATCAGGCAAACGCACAGGTCAAGGTGCAGTG
AAAATTGCGGTAGACATGGTCAATGAAGGACTTGTTGATGCTCGCACTGC
AATTAAGATGGTGGAGCCACAGCATCTGGATCAGCTTCTTCACCCGCAGG
TATACATTTTGTAGAGGGAGCTTAACTTATATGCAATGCAGCTGATATTC
TATCTAAATAAGCAGCATATATTTAACTCTGAGTATCAAACAGAGTCTCA
TGTATTAGTAGAATGCACGTTCTGCATTTCTAAACTTTTGAGTGCCATCA
ATATTTCTGTCAAGAGATACAAAAATCCTGGTCAGATGGTCGAAAACTTT
GCAGCAATATCTTTTCTAATCATGATAGAACATCCACAACTCCTATCTGA
TTAACCATATTAATATCTTCTATATATATGTTGCAAAATTTGCATTTGGC
AGGCAACCTAGCATAACTTAAACAGAAGAACCTGTCGACTTTGCATATTT
CTTTAAATAACAATCTTGCGTCTTTATTCATCTAGTTTGAAAATCCTTCG
GCTTACAAAGACAAAGTGGTAGCCACGGGATTGCCTGCATCTCCAGGAGC
CGCAATAGGGCAAGTTGTATTTAGTGCTGAAGATGCTGAAGCTTGGCATG
CACAAGGAAAAAGTGCCATCTTGGTAAGCTGACACTGGTTCTTATTCTTA
TACGATCTATCATTAACAACAGATAAGCTATAAGTTAGGCAAGAACACCT
TCCAGCTTTTTCGCCTTGTTTCAAATGTTTAGGTTGGACTCATTATATGT
AGTAATGATTGCAGGTAAGAACAGAAACTAGTCCAGAAGATGTTGGTGGT
ATGCATGCTGCTGCAGGGATATTGACTGCTAGAGGGGGGATGACTTCTCA
TGCAGCTGTCGTAGCCCGTGGCTGGGGAAAATGTTGTGTTTCTGGTTGTG
CTGACATCCGTGTGAATGATAGCGAAAAGGTATTTTGTTTAAGGTCTTAA
TGTTGATACTTGATACTGCAGAACTTCTAGTGCAGTCATGATAATGTATT
TGTTGTGGTGCAGTTGGTTGTGATTGGAGATTTGGTGATTTATGAAGGAG
ACTGGATCTCACTCAATGGTTCTACAGGTGAAGTGATAATGGGAAAACAA
CCTCTTTCTCCTCCAGCTTTGAGTAGTGATTTAGAGACCTTCATGTCCTG
GGCTGATGAAATAAGACAGCTCAAGGTACAGCGGCCAATTACTTCATATC
TTTTTGTTTAACCGATCCCTAGCTTTGTGAATGTTGCGAGATGACAATTT
GCTTTGTGAAAGGTTATGGCAAATGCTGATACGCCTGACGATGCATTGGC
AGCACGGAAAAATGGTGCTGAAGGAATTGGACTCTGTAGAACTGAGCACA
TGGTAATTTTATATTTCTTGTCTTCGTAGCATTACTTCTTCTTCTAGTCT
GTGCCAAGTGCAACAGATTTTTACCTTCAAACGTATGTTTTATAGAAATT
TAAGAACTTGTAGAACTGTAGAAGGTATAATCAAAATACAATAATTTATA
TATGAAGACTAGGCATATTACTGTTTCTGAATAATATTTTTAAGTTTTTG
TGTTGAGGAAAGATATGAAACCTGTTAAGTGACCAACTTTCCTAAAGCCT
GAAGGTGTTAGGAGGGCTTACCTGGATCATATTGTATTCTATCATTCCCC
CTCAGTTGAAAGCCCATTTTTGGGTCGAGAGTTGATCACGGGTGCAGATC
TTTCGGGGCATAAATTTGTCTTCGTGTCTTTAATAAATTATGAGGGGCTC
ACAAAAATCAAACTTGAGTCTCCCGCGCCTGAGCTCTGTCTGCTGTCTGT
CTGGTCTTGAATCTGTCTGTTGTCTGCAATTGTACAGTTGAGGTGAGTGT
TGAACAATTTAAGATCATGTTGGGGCCTTCCTCTGACACCTTAAGGTTTT
AGATAGTTACTTAACAAAACCAACACAGTTGCATTTCATATTATTATCCT
TCTGGAAAGAAATTTCAGTGAAGTTCGCATATTATTGTCTACTTCTGTAA
GGATTAAATCAACATACATTGTATACTTTAAATAAGAGAGGCCATACTTA
TTTATCAGTGCATCCTAAATTTGTAATATTAGTTTCTAAGTTATTTTGCT
TCGGGTTTTACAGTTCTTTGCTTCTGATGAGAGGATAAAGGCTGTAAGGA
AGATGATAATGGCAGTTACACATGAGCAGAGGAAGGCAGCCCTTGACTTG
TTGTTGCCTTATCAAAGATCCGACTTTGAGGGCATTTTCCGTGCAATGGA
TGGTACATTATTATCACTGATAGACATATATTATATCTATCTAATCCCTA
TATATTTAGGGGGTTGATCGCTACTATAGCAAAATTTTGGTAGGTTCAAG
GCTTTGACGAAATGAACATTAATTTCTGCTTTTGTGTTCAGATTTGGCAT
CTAGTTTACTTGTGAATAGTAACAGAGTCACGATTGAGTCTTGAGTAATT
GTTTTACTATGTACTATATGTTGATCAGCTGACTGATTTTAAGTTTCATC
TGTTTTGAGAAATTATAATAATTTATTCAATCTACAGGGCTTCCAGTGAC
AATCAGACTTTTGGACCCTCCACTTCATGAATTTCTGCCAGAAGGTGACC
TGGAAGAGATCGTTGGCGAACTAACTAGCGAAACTGGAATGAGTGAAGAT
GAAGTTTACTCGAGGATTGAGAAATTATCAGAAGTGAATCCCATGCTTGG
CTTCCGTGGATGCAGGTGTTGTTGTCTATCTCTTAAGCTTCTTAATCCGA
AGTTTCATCAAACAAGTACTTTCTCATTCTGTTTAGAATAATTCCTAGAC
ATGATTAAATGGCTTTTAAAAATAGGCTGTAGTACATTATACTGCTATTA
GTACGAATGCATTAGGCAACTTTGTCTTACTGGGGATCTCATGTACTAGA
TCAATACCTAGTGAATAGAGATGCTTGGACTTTTAAAAGGACTTGAGCAA
ATCGGTCTTCCAAAACTTGTTATAGTGTAGTCAAGAAATTTAACTGAATC
GTAATTACTGATATCAGATTCAAATGCACATATACAGGCTAGGAATTTCT
TACCCAGAGCTGACAGAAATGCAAGTGCGAGCAATTTTTCAGGCTTCTTT
GTCTCTGAGCAACCAGGGTTTTACAGTCTTTCCAGAGATTATGGTTCCCC
TCGTAGGAACTCCCCAGGCATGAATCTTCCTTTATATTTCTTCTTAATTT
AGCTTGGTATGACAAATGTATCTTAGTTTATATGCGAACTATCTGATTAT
GCTACACAATTACTATATCTATCTGCAATGCCATCTTTTGTCTGTTAGAC
TGTTACCCTCCTTTTGAACAGCAATTATGGCAAATCTCATAAATGACTGC
CCTAGTAAACTGCAGGAATTGAGACATCAAGTTAATCTTGTTCACACTGT
CGCAAAAACAGTATTCTCAGAGATGGGCTCATCCTTGAGCTACAAGGTGG
GCACCATGATAGAGATTCCTAGAGCTGCTCTTGTTGCGGATGAGGTCAGT
TGAAATGATTTGTCACTAAAGTGTTATGATATGATGCTCTCAACCTAACG
GCCTACGAGCGAATCATCATATCTTCAAGTAATACATATTGCTTATGTCT
TATATACGAAATTTATTGTAGATTGCAATGGAGGCAGAATTCTTCTCCTT
TGGGACAAATGACCTCACACAGATGACATTTGGATATAGTAGAGATGATG
TTGGCAAATTTCTTCCCATATACCTAGCCCAAGGCATTCTCCAGAGTGAT
CCATTTGAGGTTAGAAATCTAACATGAGGTCACATGAGACTTTTATTAAA
GTCAGCGGAACTATTGTTAAAAGTTTACTGTTGCTTTCTTGATATTAATA
ATGGAAAGTGTTGGCTCAGGTACTTGACCAGAAAGGTGTAGGTCAACTTG
TCAAGATGGCAACTGAAAGAGGCCGAGCAGCTAGGCCGAACTTGAAGGTG
ATTGCAATTTTATTTTACTATATGGAAGTGCTTGCAGTTACATATTACAT
ACTGGAACTTCTTATAATGAATATTTCCATCATCTCTTTGTTTCAAGTAT
CTGTTTTTAACTCATTAGGAAAATCATTTTACAAAGTACATGTTGCCACT
TTGGCATCACAAGTCCATTTCTTGTGTTCTTAGACCAATATCTGACCATG
CTTGCCAGGCATAACCTCTGATGTATACATAGATTGGATTGAGTTTCCCT
GCAGAACCTGACCATCTGAAGTTCCATAAATGTATTAATATCATCATACA
ATATAAAATCACTTTTTGGATAAAACTGTAAATATATCGTATTCTTGATT
ATGCATACCTCAGAATGATAGGTCAAAATCTTGCAATTGATAGAGTCGAT
ACTCAGTATTCTCCAACTGAATTCATAGCACACTGTAGACACGTACAATG
CCCGGCTCCAATGTATGGGTATGGTACTGCAGGATTTACAGTTATTTACA
CTACCTTAAAAGCAAACAATGGAAAAAATTATGGAAGCAGTTCTAAGATT
GCAGTCTGTGAATTCAATTTTCTTGTTTGTTGAGATCTAAATACGTATAT
GATGATGACAAACAGGTTGGAATATGTGGGGAACATGGGGGAGAGCCATC
TTCCGTTGCTTTTTTTGCCCAGGCTGGGCTGGACTATGTCTCTTGTTCTC
CATTCCGGTAACAATAAATCTAGTAGTCCTGTTTTTTCAACAATACAACT
ATGCAACTGAATTTCAACTGCCGATTTCCTTCGTTGCACTTGTATCTTTG
TTTTATTTTCTCAGTATAAGTTTTCTAAAGAAAAACATAAAACTTGTATC
ATCTTGAATGCAGGGTACCTATAGCGCGGCTAGCTGCAGCGCAAGTTGCT
GTATAAGAAGCAGTGTTTTGCAGTTTGGAATTGGGACTGAACTCTAAATT
CGTCGAAAATGTTGATCTTGAATTCTTGATCAGTTGTATATAAATAATCA
CGAATAAACACATTCATCTAAAAACACACGTCATGCTGGATAGAAAAGAA
ACGGCAAGAAAACTCTATCATAACATAAACAAACAGAGGATTGTGCATGG
TTGTAAATTATCATCATTCAACTATAAGGCATGCTTGCGGAGCAACAGTA
TTGCTCTCTGTACATGCTATGTGTGTTCTCTTAAACGCTAATAAATCAAA
ATGTGTATGTGTGTAATACTACGAATCTAGCTAATAAAAGTTATTTATAA
TTTTTCATTCTA
Sequence Length: 
8862
Sequence Checksum: 
a30c2679047ed65596b745f25a2de919
View location in JBrowse: 
DCARv2_Chr7:114780..123641-
Gene: 
LOC108196248
Gene Biotype: 
protein_coding
Gbkey: 
Gene