| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017385424.1, is a part of gene, LOC108213613. |
| The genetic_marker, MK007387 TP131799, is located in gene, LOC108213613. |
| 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_017385424.1 | XM_017385424.1 | mRNA | DCARv2_Chr1:14052264..14058234 |
TGGTCGCTCTAAATAAACTTGTGCACTCTCCTGCTTGTGTATAATAGTTG
GGTGACTACTAAACACAACAGGGGCGCCTCTATCTTCATTTTTCCCGCCA
AAACCAAAGCCCAACTTAATCTTTTTTTCCTCCTGTACTTGAACAATTGG
GTGTAGATTTGATTGATATACCCTAGATTTAGCAAAAGAAACAAGACCCA
GAAGTTGAAAAGATGAGAGGAGGCACAGTTCAGATCAATTGGCATGACAC
TAAGCCTGTTCTAACCCTAGATTTTCACCCCTTTTCTGGGCTGTTAGCAA
CTGGTGGTGCTGATTTTGATATCAAGGTACCAAAGTTCTCATCTTCTCTA
TTTTCTAATGTTTTTATTATATCTGATTGTGTTGTGTAAAGTTTTGGTTT
TAATTTGTGATGGGTTTGGCTAAAATGTGTGTGTAATTTTTGGGTGGGTT
TGTTTTTTTTGATTATATTAAATGGGTTTTGTTTGTTATGGGTGTAATTG
TCAATTTTTAAGCTCAATTAAATAGATTTTATCTGTAAATTCATGATTTG
GCTTAACTAGATTCGCTCTAGTGAAGGAAGCCGAAATACTAGATCGATGC
TACTTGAAAGTAGGGTCTTGGAGGGTGGGATGTACGCTGATGTATGCTAC
TTAGGAACTAGAATTGTTGTTTTTTAGGAAATTTCGGGACTATGGTGCCA
TCACTTGTTCATGTAAACTTTAACCCGAGGAAGTTATACTGCACCTTTTA
AAATTTATTCAATGTGTATTGTGTCACTCGCCGTTAGAACTATGTAATTA
TGAGGTTGGGCTAACAGTTTGAACTCTATATAATTTGAAATAGAAGTGTT
GCAAAATGTTGTTTGGACTTTCATTGGGATTTTTAAAGATTAGAAACTCA
GTATGGACTTTGTGATGAGTTATTCTATTGGTTCTGATCTTTTCTTTCTT
TATACAATTGAATTTTCAGCTTTGGCTAATAAATTCAGGAGAAGGGGAAA
AGAAAGTCCCTTCGGCTACTTATCATAATAGTCTTTCTTATCATGGATCT
GCTGTAAATGTTCTTCGATTCTCCCCTTCTGGTAAGAAGTTGCTTGTTTT
CTCATGGATGATGTTATTACTGGGAAATGACGACGGCAACTATAATAACT
ATTGAACGCAAGCTGCAGTTAATATTTCTAAGTTGCATGCTTATGGTGTA
TGTATATATATATATATAGAGAGTTTTACTCCAATAGAAACCTCCTTATC
CTAGAAACTAAAAACCAAACTGAAATATCACTAAATCCTAAAGCAAATAC
CACTAAATTTTTAAACAACCCCATCTCCACCTCCATCTTCATCAAACCCA
CCACCATCTTCACCAACCCCACCTCCACTACCACCACCTCCGTCGTCGCC
TCCTTCATAACCACTACCACCTCTATGCCGCCCACCCCCTCCATAACCAC
CACCTCCATCTCCATCTCCACCTCCACCTCCATTATTTCTTTAACAACAC
AACCTCCACACCTCCATCTTCACCAGGCCCATCTTAATCGCCGCTTCAAC
CTCCTTCAGATTCGTTCATACTTCTTTCTCCACCTCGACTCAACTTCAAA
GGCGGAGCCGCCACTATTCCGGCAACGCTCCAACCCCCTACTTCAAGCCG
CCCAAAACCTCCGCTACAATCATCTTTCCTCCATCTCCACCTTCACCTCC
GCCATCTCCACCACTATCACCATCATCTGAATCAAAAACGTGAACAGATC
TGGAGATTCTAAGCTGGAACAGATCTGGAGATTAAGTTATCACTAATTTC
TGCAACACATATCACTAAATCCTAAAGAGAATATCACTAAATTGTACTGA
GAATATTATATATATATAGGGTCTTACTCTGGTACAAACTTTCTTAGCGT
ACAAACTACAAACTAAAATAAAAAATCTCTAAATCGAATCGAAATATAGT
ACATATGGTATGCAAATTGATCGTTGGGATATGAATAAAAATTCAGTGAA
GTCGGATTTTGAAAAAAGTTTACCAATTAACGGGAAAAATTAATTTAAAA
ACGGAGGGGATTAGGTGGGAGTGTGTGTGTGAGGGTGTATTTGAGTTGTG
TGTGGTTGCCCCTGCGGGGCCGTTAGATTAAATGCATCCAATGGCTGAGA
TTAAGGTTTGTAGTTTGTACACTAACTTAGTTTGTATTTGAGCACTTCCC
TATATATATATATATATATAAACTTTTGGTCTGATGAATATGAAGCATAT
GGGAGACACGACATCCTGGTTTACTTGTATGATTAATGAGAGGCATGTTA
ACTATGATGACTATCAAATGCAGTTAATATTTTTATTTTGCATGCTTATG
TTATATATTTAAAGTCTTGGCCTAGTGGATACCAAGCAGTTGGTAGAATT
GATTATAAGCGATATCCTAAATTGCTTGTATAATTGATGAGAGGCATGAC
TTTAGGTATTAATACTTTAAAGATTTTAGTAGTAGTGTAGTACCAAGGCA
AAGATTCGAGCAGTATCAAATCAAGAAGTTGATAATATGTGTCATATTGA
ATGTTCTTATTTCAATTGACTTTCTTGGTTTAGTAGGGATTAGTAATTTA
TAACAAGCTCCTTTTACCTTTTTTCTTATGACAGAGGTAGCCTCTATCCT
TTTCAAAAGTTATAAAAGGATGGTTAAATATGCGGGGTCTTATACTTTCG
TACGAAACTTTAAGTCACACTACTCTAAGCTATAGACATTTCACAACTTT
TTTAGGTTCAGATTACTAGTATGCACAGAATTTCAGACGTGTCAAAAAGG
GTTGGTATTTCGCAACCAAACAAATCAGTTGATGCCAGTGATGTTAATTA
GATGAGAATTGCTTATATCACTCACCTCAGTTTTTCCTTGAGATCTTAAT
TATTTTTTAAAATCATACTTGAATTATTTTATTGTTCTTTTTGACAGGTT
TCTCTTCATAAAACATGTCTTGTATGCTATAACTTGTAAATTGTAGGAAG
TTCCCACTGTATCAGGGAAGGCGTATCTGTATAAATTTACTATCTCCTAC
TATTAAGTGTTAAACATTTGTATTGGTCCGATGGTTTATTGGCATGCAAT
ATAAGAACTTGACTTTGTTCCACACTATATATAGACCTCACTCCCATCTT
TCAAATTTATCTTCCTTATATTGTTTAGTCTGCACACTTATGCATTTAGT
TGTCACACTTGCAACAAATATAGGGCTTCTGGGGCTGTTTGCTCCTGATT
TCTCATCACTCACGAGTACTGGCATTCTAGCTTCCTTAGTCTTTTGGTCT
TCTACCTATATGATCCTTGCTTGGTTGATATAATTTTCTATCATCTGATA
ATTAATTACANGGTCGGAAGAAATTAATGTCATGCTTCACTAATTTGGAG
CTAATATATTTGTAACTTATGCAGGGGAAGAACTTGCCTCTGGTGCTGAC
GGTATGATTTGATTTACTTCATTTTCAAGTTTCTATTACAATAATAATCA
AACAATGTTTTTCCTTAGTTAATGTAATTGAGGTATGCTATTATAGGCGG
TGAACTGATCTTATGGAAGTTACATTCCAGTGATGCTGGTCAATCATGGA
AAGTCCTAAAGACATTATCGTAAGGCTTGTCATATTTATATAGAACAGTT
TATGTCAAGTTTAAAGTTGCCTCAAACTTTTAGTTAACATTTTCTGGGCT
TGTTGAGAATAATATTTATGATATATTCAGTTGCTAGACTTATTAGTTGG
CAAGTGTTTGCTGCACAGGTTTCACCGCAAGGATGTCTTGGACCTTCAGT
GGTCTACTGATGGGGCATTTTTAATATCTGGATCTGTAGATAATTCTTGC
ATAATATGGGATATGAACAAAGGTGTGCCTTCCTGTAGCTTATGATGTGC
TCCTGTTGCCATAAGCTAAATTATATGTTCTGCTCTCTTTAGGTTCTGTT
CATCAGATTCTGGAAGCTCATTGCCATTATGTTCAAGGCGTGGCATGGGA
TCCCCTGGCCAAATATGTTGCCTCACTTAGCTCTGATAGATCGCTTCGGA
TATGTGTCAATAAGCCAACTAAAGCAAAAGGAATCGAGAAGATGAACTAT
GTTTGTCAGCATATCGTTACTAAAGTGGATCTTGAAGTTGTAGATAATTC
TAAGGTTAGAATTTATTTTACCACTTTCCACAAGGCGAACTATATGTAGA
TTCATTATGATTAAAGATTTACTGCTGAATGCAGTCTGCCAAAGGCCATC
TTTTTCATGACGAGACACTGCCATCTTTTTTCCGGAGATTATCCTGGTCA
CCTGATGGATCATTTTTACTTGTGCCTGCAGGTAACACCCTATTTCTGGT
TATTTTAGCTACACTCTGAGATCTCTGTTTCATACCCCTTCAGTTATTGA
AAGCTAAAAGCACCTGTATATTTATTTGCAAAAGATGTTTTTGATGTGAA
ATATTTTATGATTGCAGGATCCTACAAAATTTCACCTGTTTCAGAACCAA
TAAATACTACTTACGTTTTCTCTCGAAAAGAACTTTCTAGGTAAGATACC
GACAAACAATTTCTTATTTTAATTTTTTTAAGACTTGTTAGTAATTAGTC
TGTCACAATAGTTACGTTGGTATTAAGTCCAAGTTGCTTATAGTGTCCGC
ATATGTTTCTCTGTTCGAAAGAGATCCTTGGAGGTCAATTTCAGCAAAAA
TTAAGCATGGGTCTTGTTAAATGTTTTCTGATTGTCGTAGATCTTCAAAT
TCTTATGATTTGCAGACCAGCTCTTCTGCTCCCTGGTGCAAGCAAACCTG
TTGTTGCAGTACGCTTCTGCCCTAAAGCCTTTAGTCTGCGTGGAACCACT
GCATGTAAATTTATTAATTAGATTTTTTATTGTTTTTGTTTTTTGACAGC
TAATTATCAAGTCTATCTCTTTAAAGACTTGTCAATAATTCCACTGATTT
ATTGTCTTGTGTGACTTATGCAGCTGCATTCTTCAAGCTTCCGTACCGCT
TTATTTTTGCAGTTGCTACGTTGAACTCTTTATACATTTATGATACAGAA
AGTGTTCAACCAATAGCAGTATATGCTGGACTTCACTATGCAGCTATAAC
TGACATCTCATGGTAAATATAATATTTGATGAATTGCAGCATGCCTATTG
TTATCACTTGCTGACAAGCAAGAACTTGCATTGCGTTGATTAGATTCTGA
CATTGTTGTTTGTTTTAGGTCACCTACCGGCAAATATCTCGCAATATCTT
CCCAGGACGGTTACTGTTCTTTAGTAGAATTTGTGGATGATGAGCTAGGG
TCCCCCATCTATTCATCAGGTAACTTGAAGTTTATTGTAGTTATGTTTTT
GTTAGCTTCGATTAATTTCCAATTTTCAGCTATATTTTCCTCTTATGATC
TCCTCTTGGCCCTCCCTCCTGTTTTTGTTTCATGACACCACTTAGAGGAT
AAAAATGACACAAGTAATGAGTTTACTCCTACAAAGAAACCCGAGGATGT
CAGGATGACGGAAGCAACAACACGTAAAGATGAAATTTGTAGAGATGCTG
AAGCAGAAAATGGTGCTGGGAAACAAGCAATTCCAGCTGAGAAGAGTGAA
GATAACCAAAAATTGCCTGCAGAAACTGATGCAGTGAAACAACCATCGCC
AACTGGAGACACTAATGAGCAGAAACAAGAGTCGCCAAAATTAGTGAATA
CAGCCACTGAAGGGAAGCCTGCCAGGAGGCGAATAACTCCGATGGCAATT
GATTGACCACAGGTCCCCATGTCCACATCCAATTTTGTATATCTTCACTA
ATTCTATTCCCATCCTAGAAGTCAATCTACCCTTGTACTAATATTTCTTC
AAATCAATTTTCTTCTGTAGCATGAATCGTTTGTGAGACTGGTGAACAAA
TAGGAATGAAAAGATGTAATCAAGATATTAGTATTTTGGACATGTATACG
GATAACGCATAAGCTCTAAA