LOC108227548

Resource Type: 
Gene
Organism: 
Daucus carota subspecies sativus
Name: 
LOC108227548
Identifier: 
LOC108227548
Cross Reference: 
NCBI Gene
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017402752.1, is a part of gene, LOC108227548.
The genetic_marker, MK005218 K2662, is located in gene, LOC108227548.
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_017402752.1XM_017402752.1mRNADCARv2_Chr6:16258435..16265667
Sequence: 
ACTCGGCCACGTCTAAGGTCTAACGGGTGAGGCAAGGCAGCAGATTAAGA
TAACGAGAAGAAAAGCAGCGGAAATTGTTTAGACAAACCCTCCCTCCGCG
CTTTTCATTTCTCTATCAAAACCCCACCCACCCCTAGATTTCAGACCACT
CTCTCACCTTCCCCTAATTTTATTTTATTTATTTTCAATCTCGTATCGGT
TTCGAATTGGCCGACTCAATTATGGCCACCGGAGATCTGGATCTCATGCA
TCCCCCTCCCCCTCCCCCTCCCGCCGACTCCGGCGCCGACGCCGGAAAAG
AAGCGTGTTCGATTTGCCTGGACGTTGTCTCCGATAACGCCGATCGATCC
TTCGCCAAGCTTCATTGCGGCCATCTCTTTCATCTCGGTACCCATTTTCT
TCATTCCTTTTATTTCTTATCGTTATTGTTTTTCTGTTTGTTTATGTATC
TATTTATCTCGAGCTCGTGCGATTTTTTCGTTCACTATGATGTAAAGTAG
TAGCTGTTGATTGTTCTTTGATTCTTGTATACTATGCATCACTTCGAGCT
TAATGCTGCTGACGTATTTATAATCGAATTGTATTTAAGGGATTTTTTCC
GGTTTTTTTGTTCTGTCTTGAGTTGTATGTATGTGTCCGTATTAGGTCAA
TTAATTGCAATTGAGTGTCTATAAGTGTTATATGCTGTCACAGCCTTCTT
TCTCGCACCAGAATTGATTGCTATGTCTTTGGCTTTGTCGTGCTACTCTT
TTTCAACTTAATAACACCTTATCCTAGACTCCACTATGGTACATATGCAA
ACTCGAACTCTGCCACCATGAAACCCCCTATGTCATGGAAAGCCCAAGTT
TTTCAGTTGTTATTTAGCTATGGACTGTTTTTATTTCCATGTTGTTTTTA
GGACCACTAATGGAGTATATCACGTGGAGTTGCAAAAGGTGGTTTGTTCA
AGCATTTATTGGTGACCGTACATATTTTTTGTCACAAGTATCTAGGCCAT
GAATCTAAGGAAAAAAGTTCCCTTGTTAGTCGATTTCATTTGCCATGTAA
TCATGACAATGTTGGTAGTCCTGAACATTGTAATGTTTGCGTATTGTAAG
AGTCATCATTTTTCTTTTTAAAAGATATTTTTAAATCTTTGCATTCATTA
CACTATTTTTATGCCAATGTCTGAGGGCCTGCAAATATTCCCTATATGAA
TGAAAATCGTTATTATCTTTTATTGGTTGATCTGTACTTAAATTACTCTT
GCATTACTGCCATAAAGTTGGGAATTATACCTTCCAAATTGCAGTGCATC
TTTCTGGTAGGCTGCCAATACCTCTATTATATAGCATATCACATTTTCGA
GTAATATTAGTAAGGTGTAACTATCCAAAATTGAGGACATTCAGATGATT
TTCCGTAGTTACCCACATACAACTTTGGAAGGTTTGAAATACCATCTGGT
TGGTGCATCTTTCTTGGGTATTCGACCACTGAAAGTATTACAATGATATT
TTCAACGGTCAAGTTTGTTAATCACAATGTTATGTATGCTTCATTAAAAG
TGTCAAGCTGCTGGAAAATTGAAAATGGAATTGGTCTATATGTATATGTG
ATCTTGTACAGATGACACATTGTTTTTTAACCTATATGGTATTTCTTGGC
CAAAATCCAATATCATGGTAATCATGATAAACAAAAACAAATTGCTGTCT
TAAGGCTACGCCTTGGTACATGCTTGGTGGATTCAACATTCGTTTGGAAA
ATCGGATTTTTGCTCTGCCAGTTGTGTTATTTTGTGATGACATCGGTGCC
ACAGGTCTTTTGTTGCATCATGTGCAACATTTTAGAATGAAACATATATC
AGTTGATCTACACTTTATAATCGATGCAGTTGGTATAGGTTTTTTTTGTT
GTTTCCTATGTGAATAGTCAATAACATCGATTAGCTTGCTGATGCGATGG
CGAAACTGCTCCCCTGTATTCTCATTGCAGATGGAACATTGTTTTGCAGG
GGATTATCAGACTTATTAATATTATATTGACATTCGTACTATTTTTATGT
GTAAACATTCATAATTTAGTCCTGCCATATTCTAGCAATTTGAGCTGAAG
CTTAAATCCACTACTATAAGAAGAAATACTTTACCCCCCATTCTGCTCAT
TTTTTCTTACAGTTCTCATTGTAGGAAGTTTTTAATACCATAGTTTTTCG
CTCTTATTTCCTACCTCCATTTTCCTCGTTAAAATTTTATTCCCAACTTT
GCCATTTCAGTTCCGCAGACCAAACATAACAATATTATATATAAATTACT
AGCTAACTATTCTTTGGTTTTTTTCTGAGGAATACACTTTAAGACTACAT
GATCTCATCCGTGTATCTCTTTTATCATGTATACTAGATGCTCCCGTGCT
GGATAATTGTGGAATGAATGATTAATATCTTATGGTTGTGTGCAGATTGC
ATTGGGTCGGCATTTAATGTTAAGGGAGCTATGCAATGTCCGAACTGTCG
GAAAACTGAAAAAGGTCAATGGCTTTATTCAAATGGTTCCCGTCCATATA
CCGAAATTAATATGGAGGACTGGGTTCCTGACGAGGATCTTTATGATCAC
AGCCATTCAGAAATGGTAAGAAAATCTTATAAGGCAATTTACATAATTAT
CGCTTTTGTAATTTTTTCTAGAATCATATCTGAAGCGCTATTGCGCTTTC
AGTCATTAATGTTAGAATTTAGCTTTGTTTCTTCTTTCCAAGTAAACAAT
TAGTGCATTAAAGACCTTGTAGACCACACACACATGTAAGAGGTTGATGT
ATAGTGTTGAAGATCATGTTTGTATATACAGAAAGTTTGATTGAATACTT
CTGTGGTGTGTGGGGTTTTTGTATCCAGGAAATTTTCCTGCGTAATTTGA
TTGCGGCATTGGTCAATATATGCTCCAGTTACTGCTAGGACTAGTTTACT
GAACTTTGTTGTTGTTGTTATAGTAGTTGTTATTATTATTATTATTATTA
TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATT
ATTATTATTATTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNGGGGGGATTGTACTTGCATATTTTAGATCG
AAAAGGAAAATTTTGTTCTGATATGAAGGTCTAAATTCAATGTTTTAACC
GAATTGTGATGGGGATATTTTTGACGATTTTTTAGGCTTGCTGATGCAGA
GAATTTAAAAAAGGAAAAAAAAAAGATACGTAGGAAGAGATAGATATCGC
TCTTGGTGACTAAATTTATTTTCATTGGAGTGGACCACTTAGAAATATGT
GAGCAACTGAAAGATTTGACGTAGCTCAAATGAAAGATCGTTGACGTCTT
TTAGATCAGTTGGGGAATGAATGGGGATTGGGTGTCCAATTAATAATTAA
TACTCCCTCCATACCAATTTAGATGAGCCTTTTGCTCATTTCACACATAT
TAAGGAGTATTAAAGGGTTGTTCCTTTTTCCATCTTTACCCATACTTATT
GTGTTGACTTCTTTTGTATATTAGCTAGTGGTACATTGAAAATGATAAAT
AAGAGAGGGTAACAATAGAAGATTGTTGATAAATATGCATAGAAAAGTGA
GAGGCTCAACTATTTTGGGATAAATTTTTTTCTCAAAAGGGTTTTAAGTA
CAGAAAAGAAACTATGGTCCTATAAGTAGGTATGACCTCAATATATGCCT
TCCCATTTTTATCAAAATAAGTCTGTCTATTTAGGCTCAACTATTACTTT
AACTGTTTCTTTTTAGTTATTTGTCGTCATCCCTAGACAAATGTTCCATG
ATTGCTTCAAGAACTTTTGTTTGATTTTCTTGGCTGGTTTAGTAAACCTT
AGAAGCGGGTAAGCTGTTAGCTGCTGTTCGAAATCACTTTGTTTGCATTT
GCTTGCTGTTCATGATCAATACTTAGCGGTCTATTGCTTGAACTATGATA
TGCTCTCTTACACATTGATGGTTGCATCATTTTTACTGCTAACCTTTCGA
GTGAACTCATTCCTGCAGCAAGGCTGCTTTTTTCAAGTTTTTGACAGTTA
ATGGTTGCTTAGTGTTATTCTTTCTTCTAGAACTACAAACAAAGTTTTTT
TAACTTCCGAAATCATAATGGCTAATATATTTTTTGTTGCTAATCTTTGC
AGTCGTTTGGAGTTCACTGGTGTCCCTTTAGTGGATTAACGCGACATCCA
TCATCCTTTGAGTAAGCACACATTCCATCTGAAAATTTTCTATTTTTGCC
TTGGAATGTTTTCATTTCATTTTCGTATTTTAATTCTTAGAGCTGTGGGG
GTTATTTTTTTCTTTTCCCCAGTTTTTCTCTGAGTCCTTTCTATGAGCAA
CTTTATTTGTTTTTTGCATATTCCAAAAGCTGTCTATTTTGCTCTATTAG
ACTCTAGCCGATGGAAGTACATAAGTAATACCAATGAGCACTTGCACTTA
GCTGACACAAGTAATAATTAATAGATACTAGTGTTTAAGTAACACTTAAC
TTGCATATATTGTAATATAAACCATGTAAATGTTTACCAGCACTCAGCAT
GCACAAAGCACAATCCCTCTGTTGATACCGGTGTTTCAAAAAAAAAACCT
TGTTTTACTAGTTACGACCCTGAAATGATATGGATCCAAGTATGTCTATT
ATAATTTTAAAAAAAAAGTCTGTCTATTATATGTAGCCTATATAAGGCCT
GGGACAGGGAGTTGAGAGTTAATTTATCTGGATTCCAAGTTAAGTGTGAG
AGGCTCTCTCACAGACGAGTCTTGTTCAGACCAATACGATATAGACTCAT
CTAAACATTCTTTTGTGTCAAGGCGTGTGACTAGATCCTACGTCAAGAAA
CATAACACTAGGATTTCTTCTTTATATTTAGAATTGGAAAATATTCATTG
TTCAAATCATATATATTTTTCTGACATCGTGCTTTTATTATCTGCAGTGA
AAGTGATCTCTCGCCAATTCCATGTAAGTTTAGTTTTTTGTGTAATTCAT
AGTACTCTGTGACCTTTAGCAATTATAGACCTCTGTTTTCTTTTTGTCAG
ATCATGACCTTCTTGGACAACATGCTGTATTTGCTGAACATGCAGCTGTA
TCTTCTGGTTCTCATCATTGCCCATATGTTGCCTACTTTGGACCTTTTCC
CTCATCTTCAAGTTTCAGGGGAAGTGTTTCTGATGGCTCTACTTTCAGCA
GTCACTGGAACAGCCGATCAGCTGCAAGTGAGATGCCCACCTCTTATGCT
TTTCCCTCTGTGGATGTCCACTATCACAGTTGGGAACAGCAGTCATCTCT
CTTCCCTACAGCAAGCAGCCGCGTTCCTGGTCCTGATCAGGCCTCATTGC
CATCAATGACCCAAAGGGCAGCGAGGAACAATTTTGATAATCCAAGACCA
GGATCTTTTGTCCATCCGTTTGCTGTTGGCCATGGCCATGGGTAAGCTTA
AACAACCTTATTATGTTATATCACTATCAGGTAGCTTGATTCCCATAATT
GTTCTGTATCTTCTGTATGTGAAACTGGAAAAGAAAATGCTTTGTGGATA
GTGTTTTGACAAAAGCATATTAGAATGCATCCAATCTGCGGGTCACTGGC
ATCCTATCTTTTCGTTACCGCTCCGTGGGTTGTTTAGGACGAGCCAAATT
TAAATCAAGTGCATGTTTTATCTCTTATGTGGGTTCATTGTTAGTTTTTA
TAAGCTTCATTCTGGCAATGTAATTTTGAGTCATTGTGCTGATTAAGTGA
CCCACACAAACCAATAAACGGGCAGTCATTTGTGGAGTATAAAATATAAT
TTTAAAAATAAATGATATTTTTTGTAACTTCTTGTACATTATTAGCACGA
CTTCATTGAATGAATCTGTGTAAAGTGTCGATACTAACATTTAGTATCAT
TGAAGAACTGTTGAATTATTCCATTAGACATCCAAAGCATGTGCATCTCT
TTCAATCTTTTTGTCCCTTTCCATTTAGGATGTTAAGTTTTCATGTGATT
AATAGTTCTAATGCTAGGTCTGGGAGCTCGATTGCTGCCTCAATGTTTCC
TCCATACCCTGGCAGTGTTGCTCGTGCCAGGGAGCGGGCTCAAGCTCTTG
AGGCTTATTTCCAGCATCCTCCTGGCAATTCACAAGGCTTACATACACCG
GTCATGCCCACCCTGCGAAGGTCCAATGGTCACAGGAACATGGCTCAAGG
TGATACACTTGCCTTGTCAATTGAGCACGGCAATGGCTTTTACTTCTTAT
CATCAAGCCCAACAGCAGGAAGAAATTTTGCAGAAGCAGATAACTCGATG
TCAAATCATTTCTATGCCTGGGAAAGAGAACAGTTTCCTTCCTTTCCATC
AAGTGAATCTGATAGAGATCCTATATGGGGGCTCGTCCATCATCAGCTTC
CAGGTGCCCCTGACACCGGCATCAGGCCTGCCAGCTTTCGTCAGAGGCAT
GGATCTGAAAGAATGACATCTCAGCACCGGTCATAGACTTGTCCTGCTCT
TGTCGCTTCTGTTGATTGAAAGTATCATTGCTATGACTTTAAACTTAACA
ATTTGAATGTCCCGAGTAATGGTATGTTGTGATGTTTGCTGTCTGTTAGG
CAGAAACTGTGACTGTTTGTGGCCCCTAGAAACGATCTATCTTGGCTGCC
ACCCGTGGTAGTGGAAATTGGCTATTGCTGGTTTCTGCTTTTAGAAATAA
GGTGATTTGGTGAAGGGTAAACAAAAGAACTTCATCCTTTGGCCTTTGAT
TCACATTCACTCTGTATATATATTATTTAAAGGACCTGAAGTTTTAGACT
CTACATTGTGTCCAGCTTTCTGATTTTCTTTGAGGGGAAATATATTTAGG
GTGCTGATTTATGCGCACCTTAAATTTGTTTA
Sequence Length: 
7232
Sequence Checksum: 
f3783cf4db0ae1485104cbcb7aecd07a
View location in JBrowse: 
DCARv2_Chr6:16258436..16265667+
Gene: 
LOC108227548
Gene Biotype: 
protein_coding
Gbkey: 
Gene