| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017367026.1, is a part of gene, LOC108199276. |
| The genetic_marker, MK004816 K2260, is located in gene, LOC108199276. |
| Name | Description |
|---|---|
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 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 | |
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. |
| Transcript Name | Identifier | Type | Location |
|---|---|---|---|
| XM_017367026.1 | XM_017367026.1 | mRNA | DCARv2_Chr8:27000138..27005892 |
CTCTTTATTATATTGTCTAAACTCCAGATCTCTATCTTTGGCCACACGTC
CATTCTCACCTCAGATACTCTCTACTTGTATATAATATAATATACACACA
CATACTCAACAGAGCTGACACTTCTTCTTCTTGATATTGATTGGTTGAGT
TTTGCAAGCTTTTTCATGAACTAAACCAAGTTCATGTTATTCTCATCACT
TCTTGCATAACCCCTTTTAACCATGAATTCTTGGAATGTTTGTATCTTTA
CTTACAAAAAGATGATACTAACTTATAGAAGGAAATAAGCCCTTTTCTTG
GTTGATGAGTTGGGTATTTGATACATGGTTTGAGTGAATTATGGTGGTGA
TTTGAAAAGGGTTTATCAAAGATTTGATCTTTTTGGTTTGGGAGTGAGGA
AAAGTGTAAATACATTGAGTTTTGTTTATACTGAAGTTGATTCTGTGATT
GTTTTTTTTGTTTTTGTTTCTGTGAAGAAATGGCATCAGGGAGCAGCAAA
GCATCAACACATTCACCTATGAAGCAGAATGAGAGCCAGACTTCTGGTCA
GGATCAAGGTCAGTTTTCAGGGACTCGAAATGTGAGGGAGACAGTTAGTA
AAGCAGTGGCTCAGTATACTACAGATGCTAGGCTTCATGCTGTGTATGAG
CAATCTGGAGAGTCTGGTAAATCTTTCGATTATTCGCAGTCTATTAGAAC
TGATAATGATTCTGTACCTGAACAACAAATTGTTGCATATTTGTCTAAAA
TACAAAGAGGGGGTCTTATTCAGCCTTTTGGTTGTATGGTTGCTGTTAAT
GAGTCTACTTTTCAAGTTATTGGTTATAGTGAAAATGCAAGAGATATGCT
TTGTCACTCCCCACAATCAGTCCCTAATATTGAGAAACCGGAGTTTATTA
GAATTGGAGTGGATGTGAGAACGCTTTTCACTCCTACGGGGGCAGCTTCG
TTGGAAAGGTCTTTTAGGGCTCGTGAAATTGCGTTGTTGAACCCAATTTG
GATTTATTGTAAGAATTCTAGAAAACCATTTTATGCAATTTTACATAGGA
TTGATGTTGGGATTGTAATTGACTTGGAGCCTGCAAGGACAGAGGATCCT
GCTCTGTCAATTGCGGGGGCTGTGCAGTCACAGAAGCTAGCTGTGCGTGC
AATTTCACATCTGCAGTCACTTCCAAGTGGAGATATCAAGCTTCTATGTG
ATGCTGTTGTTCACAATGTGAAGCAGCTTACTGGATATGATAGGGTCATG
GTTTATAAGTTTCATGAGGATGAACACGGTGAAGTACTGGCCGAGAGCAG
GAGGCCAGATTTGGATCCTTATCTTGGATTACACTATCCTGCAACTGACA
TTCCTCAGGCTTCTAGGTTTCTGTTTCAGCAAAATCGGGTTAGGATGATT
GTGGATTGTCATGCCACATCAGTTCCCGTAATCCAGGATGATTCACTTAT
GCAACCATTGTGTTTGGTTGGTTCAACTCTTAGGGCTCCTCATGGTTGCC
ATGCTCAGTACATGGCTAACATGGGATCAATTGCGTCATTGGCTATGGCA
GTTATTGTCAATGCGACTGGTGAGGAAGGTACGCGGGGGAGGAACTCTAC
CAGACTATGGGGATTAGTTGTTTGCCATCACACGTCTGCTAGAAGCATCC
CATTCCCACTCCGCTATGCTTGTGAATTTTTAATGCAGGCATTTGCACTC
CAACTCAATATGGAATTGCGACTGGCATCCCAAATGTTGGAGAAACATGT
CCTAAGAACCCAAACCTTGTTGTGTGACATGCTCCTTCGAGATTCACCTA
CCGGCATTGTGACAACAAGTCCTAGTATTATGGACCTTGTGAAGTGTGAC
GGTGCTGCACTTTACTACCAAGGGAAGTACTGTCCATTAGGCGTGACCCC
AACTGAAGTTCAGATAAAGGATATTGTAGAGTGGTTATTGGCTTTCCATG
GGGATTCAACTGGGTTGAGCACTGATAGTTTGGTTGATGCTGGATATCCG
GGCGCAGCATCACTTGGAAATGAAGTTTGTGGGATGGCTGTTGCTTATAT
CACCTCGAGGGATTTTTTGTTCTGGTTTCGGTCTCACACGGAGAAGGAGA
TCAAATGGGGTGGTGCAAAGCATCATCCAGAGGACAAAGACGATGGTCAG
ATGATGCACCCACGCTCATCATTCAAGGCATTTTTGGAAGTGGTAAAGGG
CCGTAGTTTACCCTGGGAGAATGCTGAAATGGATGCAATCCATTCTTTGC
GTCTTATTCTACGAGACTCATTTAATAATGCGGAGGAGAGTAATCCTAAG
ACAACTGCACTTGCTAAGGTGGAAACCACTGAGTTGCAAACTATTAATGA
GCTCAGTTCAGTTACTAGAGAGATGGTTAGACTGATAGAAACTGCAACAG
CTCCCATATTTGCGGTGGATATTGAGGGCCGCATAAATGGGTGGAATGCA
AAGATTGCTGAATTGACAGGTTTGTCAGTTGCGGAAGCAATGGGAAGGTC
CTTGGTTCATGATCTTGCTTATAAGGAATCAGCGGAAACTGTTCACAACC
TGTTGCATAATGCATTAAGAGGTATTTCTTTCACATCTAATGTCTGCTTT
ATATATTTACAAGACATATAGATATGTAGTCCTTTTTTCAAAGCCATTGA
GATTCTATGATATATGTAATGTACATCAGAAAACATATTATTGCCTTCTA
ATATGGTGGTAGGCTGTTATTATTGTCCTTTACAAGATAAATTTCAACTA
TAGGTTGGTATATTTTGCAATAAAGCACTACAAATCCACATGCCTCCCTT
AATAAAGTAAAATTCAGAATTAGTTCTTCCATGTCAATGTAATTTCTAGT
TTCTACTGTAAAAGTCACTTTTATAGGTCACGAGCTTATATGCAAGTTGC
TAACTTCATATTCTTTTACCAGTTGTCATTGTTGTGATTTGACTATATTT
TAAACAATGAGGAATTATATGAATTTTTGGTACATTTTGTATTGGTCAAC
ATACTGGTACAGAAATGCAGTGTTTTGTGTTGGTTATATATTGTACTAAG
TCATATTCTCGCAGGTGAAGAAGAGAAGAATATTGAGATAAAATTGAAGA
CAGTCAATGGGGAAACAGATAGTGCCATCTTTCTTATAGTGAATGCTTGT
TCTAGCAAAGACTACACAGAAAATATAGTTGGGGTGTGCTTTGTTGGTCA
GGACGTTACTGTTCAGAAAGTGGTTATGGACAAATTTATTAACATACAAG
GCGATTACAAGGCTATTGTTCATAGTCCGAACCCTCTGATTCCGCCTATA
TTTGCTTCAGATGAGAATACGTGTTGCTCAGAGTGGAACAGGGCAATGGA
AAAACTCACTGGTTTGGGCAGAGAGGATGTCATCGGGAAGGTGCTGGTCG
GGGATGTTTTTGGCAGCAGTTGTCGGCTGAAGGGCCCAGATGCTCTTACA
AAATTCATGATCATCCTGCATAGTGCAATAGGTGGACAGGAAACAGATAA
ATACCCTTTTTCCTTCTTTGACCAGAGCGGAAAGTTCGTGCAAGCTCTTC
TGACTGCACATAAGAGGGTTAATATGCAAGGCCAGGTCATAGGAGCTTTC
TGTTTCCTGCAGATAGCAAGTCCAGAGCTGCAGCAAGCTTTAGAAGTGCA
GAGGCAACATGAAAATAAATCGTATGGAAGAATGAAAGAATTGGCTTACA
TATGCCAAGAAATAAAGAAACCCCTTAGCGGCATACGATTTACTAATTCT
CTTCTTGAAGCCACGAATTTGACTGAAGATCAGAAACAGTTTCTTGAGAC
TAGTGCTGCCTGTGAGAAACAGATGTTAAAGATTATAAAGGATGTCAATC
TGGAGCAGGTTGACGACAGGTTTGTTTTTGTCTGAATATCATTACACAAA
CTGAAGGTTTTTAGCACCGGTGCATACCATTCTTGTCTATTGTTGAACAT
TCTAGTATAGATTACATATATGCTTACGTACAGAATGCTGCATTACGTGA
AACCAGGAATTTTTACCTACATAAATAATGCTCTACTGGAACTCCAAATG
TTTTATAAAGAGAACAGGGAACTTAGAGTACTGTAAACTTGCCGGCAAGC
AGTTAACTTTAAGCATATATAGGCTAACAGATTGTAAACAAGTGAAAGTA
TTAATTTATATGATGCAATATTGAAATCTATATTCATTTAATAACTCCTA
AGCTTTAGCGGACCTATTTGTTAATAAAAACTTGTCAGTGTTCAAGCTTG
TAAAGAGTAGGACTCTAACTTACTGCTAATTACTGTAATATGCTATGCGA
AAATTTATAATTAAAACATTATTTTTTTTGCACTAGATTGCAGAACATCT
AACACTATTTTAGCATTTTTCTCTATTTTGGAAACACTCTAATTGTAATG
AATTTGTTACTCATATTTATTTCTCATGTTCAATATTCGTCATTATTAGC
TAATGAATAAGTTTTGGGTTAATCTTACACTCATATTCGTTTCTTATGTT
AGTTCTTTAGAGCTTGAAAAGGCAGACTTCTTGCTTGGTGGTGTCATAGA
TGCTGTTGTTAGTCAAGGAATGTTAATGCTGAGGGAAAAAGGTCTGCAAC
TAATTTGTGATATTCCAGAGGAAATCAAAACACTATGTGTTTATGGTGAT
CAAATAAGAATACAACAGGTCTTAGCAAATTTTCTGTTGCATATGGTGCG
TCATTCCCCATCTCCACAAGGTTGGGTAGAAATTAAACTTCAGATTAGTT
TGAAGCAGATATCTAATGGAGTTACCAGTATGCGCAGCGAATTTAGGTAT
TCATCTTTAAATTGATTTGCAACTTCTGTTAATAATAGTAATCTAATGCT
CTTAGTTTTAAGCTTATGATCCTGAAGTTGCTTACATGAACCATCTTCTA
CAGCTGTTAGCAATCGAGAACTGATGTTGAACTACTTGAAATCACAGACT
TTGGCACTTTACATAGATTAGTCAGGCTTAGAGCTTAGTTTTATTATACT
TGAACACATGACACCACCGACCACTAGGGCTCTAACCCTCAACCTATTGT
CAGAGAAGAGGGTCATTCTGCACTAGGCTACAATGCTGGGGATTAATTCT
CTTGGTTTGGTTTAACTTGTATCCTGAACTTAACACGTTGAATTTCACTG
TGAAGGATTGTCTGCCCTGGTGAAGGCCTTCCATCCGAACTGATTCAAGA
CATGTTTAACAGCAGTGCGTGGGTGACTCAAGAAGGTCTAGGATTAAGCA
TGTCCAGGAAAATCTTAAAGCTTATGGATGGCGATGTTCAATATATCAGA
GAGGGAGAAAGATGCTACTTTCATATAATTTTAGAACTTCCTGTAAGTCA
AAATAGTTCTGGTAATGTTGGATAGGTTCCTGAATCATCCCATTATTTAG
TTCGGATAAAATCCTCTAACAAGGTATGACTGCAGCCTCCCACAATGCAA
AGCTCTTCTAATGTAATGTGCAAGTCATTCAAACAAGTATTCACTTGCTT
GCAGAAGAGCAAAGTTTCAACAATTTAGGAAACAAAATTTAATATAGGCT
AAGCTTTTATCAAGTCCATACGAGGAACTGTTTACAACCAAGTAGAGATC
CAGTAATTGCATCTGCAATTCTTTGCCCCATTGTGTAATAAGGCTATTAT
GCTCCAACTTATTTACCATTTAATGGTGAGTGTTTTGAAGTTCCCAACTA
ACAAGTAACTCTGTTTTTTTCTAATGTAGCAGATCTTATTAAAGTTCCAG
TTTA