| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017403373.1, is a part of gene, LOC108227962. |
| The genetic_marker, MK004771 K2215, is located in gene, LOC108227962. |
| 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_017403373.1 | XM_017403373.1 | mRNA | DCARv2_Chr6:27349454..27355702 |
CAACACAACACCTACTTTCAATCAGTTTGATTAGTTTAACAAAGTAAAGA
CTACTTGGCAATGCAATAAATAAGGCACCAAGCAAACAAACACAGTCTTA
ACACTTTACCATAAACAACACGAATCAATACTAGTCTGAAAACGACCGCC
AAACCCCCCTCTCCGCTCTCACTTCTCATCGCCGGACTTTCCTTTTTTCT
CCGACAACAACCCCTCCTCGTATTTATACATATAATCACCTATCGTTGTA
TTGATGCACATACATTAAATTGTGTGTGTTTGTATATAGAGAGCCAAACA
AGTAGGAGACTAAGACAGGAAGACAAGACAAGAAAGCTGATTAATACCCC
TTTTTCTTATTATTAAATACTTTAAATTTGTGAATCTGGGTTATATGAGG
ATTCAAATATTTGTTTTTTTGAATCAATGAGGATTTCAAGATTGTTTTTG
TTCCGGTTTTCTCTTTGGCTCTTGCTGTTCTTCACTCCTAAAGGTATTTT
TGCTTTTTCTACTCTTTTTTGTTTGCATCTTTATGTTGTATGCATCTATT
TAACACCTTTATTGTTAATTCGATTGTTTTGTGTATGTATTTGTGCGTTG
TTATAGAATCTGGATGGCCCTTCATTGATTCTTCAGGTTTTTATGTTTTG
ATTTTAAATTAAGTGTCTCAGTGCTTAAGTTGATCGGTTAATTGAATCTT
TCAATTGTTCGTAAGGGCTTTGGTGTGTCCAGTTGTAAACCTTATTGGAA
AACTAAGGATAAGGAGACTTAGTATTTAGTTGAAATTCTTAATGTGATGG
ACACAGGAGGGAGAATTTTTACGTTACACATAGGCTATATGGCAATTGCA
GCAATTGCAGTTATTTGTGACCGTAACAGTGTTGATCAGCGAATGTGTTT
TTATAAATATATTTGAAGACTTGATATTTTAGGGTTAAATCTCAAAGTGC
TTACTGAAGCGAAGTCGTGGTATCTAATGAGACGCCGAAAAGATCAGTGA
GTAATGTGATACCACGACTTCGCTTCAGTGAGCACTTTAAGATTTAACCC
AAATATTTTAGTGTGCTAACTACCAATAGGTTCTATATAGCGGTGTGAAG
GTTATATTCTGTTTATCTCAAGTTCATATTTCATTACATTAATAAACTAA
TATTGTTATGATTTACAACTGAGTCTACATGTGCTAAGCCAATAACTCCT
GTTTTCTTTTTAATGGTGTAATAATTAGCATGCTCAGAGACAAGATTGAG
TGCTTAAAATGCTGAATTCAACTTGATCAAACTTCAAGTCCCCTGATATC
CTTTGGAGAGTGTTGAGAAAGTTCCCTGAATTCATTTTTGCTGAACAAAT
ATGTAATTAAGAGATCAAATCATAACGACATTACTACTATAAGGAAAAGA
TGTTATAGTAAACAAATATATTCTTTCCTCTATCCTTCCTTTGCAGGACA
CTGGGCAGTGAAAGCATTTACAGGAACTTATGGGATAAATTATGGAAGGA
TTGCGGATAACATTCCCACACCTGATAAAGTTGTTACACTACTTAGAGCA
TCTAAGATAAAGAATGTACGAATATATGACGCTGATCACAGTGTCCTTAA
TGCCTTTAGTGGGACTGGACTAGAATTGGTGGTAGGCCTTCCTAATGGAT
TTGTGAAAGAGATGAGTACTAATGCAGATCATGCCTTGACTTGGGTTAAA
GAAAATGTGCAGGCATTCCCCAAGACCAACATTGTGGGTATTGCAATAGG
AAATGAAATTTTGGGTGGGAGTGATGTGGATCTTTGGGCAGCTCTGTTGG
GTGCTGCAAAAAATATATACAATGCTACAAAAGAGCTTCAACTAAAAGGT
GTTCAAATTACAACTGCTCACTCACAGGCTGTTTTTGCCGATTCCTACCC
ACCTTCTTCATGTATTTTCAAGGAGGGTGTTGATCAATACATGAAGCCCC
TCTTGGAGTTCTTTTCACAGATTGGTTCTCCATTCTGTTTAAATGCTTAC
CCTTTTTTGGCTTACATGGGTAGTCCAGATACAATTGATATAAATTATGC
TCTTTTCCAGTCAACTGATGGAATAGATGATAAGAAAAGCAAACTTCATT
ATGACAACATGCTTGATGCCCAGGTCGATGCTGCTTATTATGCCCTTGAG
GATGCTGGATTCAAAAAAATGGAGGTTATAATTACAGAGACGGGTTGGGC
TTCTCGTGGAGATGACAATGAAGCTGCAGCTACTGTAGATAATGCAAGGA
CTTACAATTTTAATCTACGTAAAAGGCTTGCCAAGAAGAAAGGGACCCCA
CTGAGGCCGAAAATGGTACTAAAGGTGTATGTTTTTGCAGTGTTTAATGA
AAATTCGAAGCCTGGTCCAACATCAGAGAGAAATTTTGGACTCTTTAAAG
CTGATGGAAGCATCTCTTATGATATTGGCTATTCTGGACTTAAGTCTTCA
TCTGCCCCTTCAACTGTTTTGTCTTTAAAGGTATGATACCTGTTCGAAGT
GTATTATTTCAAAATGTTCTTCCTCAGCTTTACACAGATTGCTCTACTAT
TTTTAGAGAAGAAAATGAAGTGATATACCGTATTCAAAAGAAAATGCTTA
TTATAGAAATATAGGATATTTGATTAATGGATGCTTGTGTGGACTTCTAT
TATGCAAGGATTATTTATGTAATATGCAGAAATTTCTTCTAGACTAATAT
AGTGGTACAACATACATCCAAATTATAGTAAAATAAACAAACAGAAGATG
TTATTACTTATTACTGGAACATGTTAGAACAGGATCTGAGTAAAAACTAT
TTTAATGCCACTTGCTGTAATTGGCTGTCTGACGGTGTGATGTTTTACAT
AAACCTGCTATAATTACCTTATATGATCAGGAACCGACACAACCTGCTGC
AAAGACAGGAAGCGGAAAATAATTTTTTTGTGATAAACTGTTTCTTTGTT
ATTAATATCGATAAACTCTATGTGAAAACCTACAACTGGTTTCAACTTAT
TGTTGCATCTAAATTAGTTTTAATCTTACATTATGTATTGTTCTTATTAA
TTTATGGATACTACTAAGTACTAGCCAGACGATGTCTTTATGATATGGGG
AAAGGGTCTCTTTGCATAGTTATAACTGCGTATTGAAGTTACAAGTTGTT
TGCTTTAAAATATATCTTATTTATATAACGTATAATATTATAATGGTGGT
CGATTGAGTTCTTATAAATTTATGATGAATGCTACATAGTGATACAACCT
TTCTTTATATGTGTGCATCTGATGTCTTGATAATGCAATTGTCAAAGACA
AGGTTTAAGCTAAGTATTTCTATTCCTTGATATGTGAAGATGTGATTGGT
TTAGGGAGACTGCCACTGTGGTCTGTGCTTATCATGAAAAGGGTCAGGAA
TTAGCGTTTGTACATGATGCTCTAGTGTCCTTTATCTTGTTAAATTGGCG
TTTAGAGTCATATCCTGGATCTTTCGAGATTTAACTTTTAGTTCAATTGA
TAATTGCTTGACTATGTATCTTGTTGTACATATATTCAGCCAAGATGTCG
AGGGAAGTATGACATGCCTATGCGTTTTGGATATATACACATGATCTTCT
CACTTGACATATGCTCCTCAAATTCCTAAAATAAAATTTTGAGACATCTT
TTGGCCTTTCTGAGACTGCACTTTTGCAGACTATTAATCTTCTATGTATT
TTCCTGAATTGGCAAATTGGCATTACAGATATTTACTAAAACAGCAGGCT
TAATCTGTTCATTCTCAGCCAACATTTTCCGTAAGTAACTAGTGTTCTGG
AGATATAACATAAACATGGGTATGCAGTCTAACCTGGATCTTCACCTCAA
CACACCAACAGTTCTTCCAATCTCAACACACCAACAGTTGCTTGTGTAAC
CTTATATGCATGAACTTCTATTTTCACCACTGAATCTTTTGCATTTTGAA
TGTCAAGTTAGACTACTTATTACACTAGTTATCTTACAATTCAAATTAAC
ACCATATGTTTGACATTTTTTTTGGAATTTTACGTAAAACATCTATAGGT
TACCTATGTTATCCACACCATGTCCTGTACTTGACTGGTTAAGTCTATTG
ATGCCATGCTTGTATACATGTATTTTCAGAATTAGACATGCATGATTGTT
GAGCCTAGGCACTTCCAAAATTAGGGTTTGGTACTTTCATCCATGAGATG
GACATAAAACAAGCTATTCCTTAATATCTGAGATATGCAGATACATGCAA
CATGTAATGGTAATATTTCAAAATCCTAAATGAAGATGATTTAACATCAT
CATCTGATAGATGAGGTTAATAAGCTAATTGATGGCCAAGGGCTCACTCC
TTTGTCCTGTCACACACATATGCTACTTTTCTGTACTCCTTCAATATGTC
AAGGTATATATTCTTAGCATTAAGCCTGTAGTGAGAGTTGAACTACAAGG
TCCTGAATTGTATAGGTCCACAATTTATGTAACAAGTGTCCCTAAATAAT
AAAAGCTATGACCAGTACACTTTTTACCTAAAATATATTTAATAGTTATA
AAAGAAATTATGAAACAGGAAAGCTTGATATTTTCAATATTTAACCTGTT
CTTTTAGGGAGCTTTACAAACACCGACACTCATTTCAGCAGTCAGCATTA
AGCCATATGTTCATAGTGGATCCTATTCAGCAGCTCCTTCTTTTCAGCTT
TTATGTGCCTGGAGTAGCAAGCTTACATATTAGTTAAATAGAGTAACAAT
GGAAAAACCGGGATTTTGTGGATGCTTTAGCCATATGGAACATACCATAG
TAGTTAAGCATTTATCCAAATTTTTAAATAGCTTTTTTCAAGTTGATTTG
CTTGAAATTGTTAGATCGCCAACTTTTCCACTACCTTAAATTGTTAGGAA
AAGGCACTAAAGAAATGATATACCTTTAACACCTCATCTCACTCAAAATT
TACCCATTTTCTTGGTAAGAGTAGATCACTAGGCAGGGTAGAACCCAATA
ACCCATGATTGAAACCTGGCCATATTTCATCATCAAAACTGATTACAAGA
TTAGAAAATACATGTAAATATACATATGGAAATGATTTTATTGACTAATC
GTTAAATTACATCTTATGCTGACTTGTATAATTCTAATTAAGCTAGCCTT
TTTTTCCGGGTAGTTGAAAATTTTTCAAAGCATCAAATGTTTAAAAATGA
TAAGATGATTCTATGCTAGCAAGTATCAGTACCAAGTGAAACTATGGCAT
AAAACACCTTAAACAGACTCGGCTGAAAGTATATAGTGCCTGTATCAAAA
ATCGTGGTGAGGAGGCACAGTCAGTTTTACAGGGTCTACCCATCTCAAGA
AACCAATCTCCAAGACTGATTAACTTTGACAACATTTATTTTTTGCATAT
AATCATAGAGGTGCATTTGCTGAAAAAATGCGTATATTTTCACAAAAATG
CATTGCAGAATTAACTTCTGTTAAGTGCATCTGGAATCATTTCGATGCAG
TGGTTTATACCTATAGATAATGGTATTATGCTATATTAAACTTAATTCCT
TTCAAGAAAAAGTAAATATCCTTGAAATTCAGATATACTGTAATCAATTT
ATTATCTTGAATAAGATTCTATAATTATCGGTAGCACTTAAATTCTTGTT
TAAATTGGTGTAGCCAGCTTTGATGACTGATTAGGTTTCCTGATAATTAC
AAAAAAAAAAATGCGGTTACTAGTTTAAGGTCTCCGTTTATTGGTAAGTG
TTTTTAAACGTAAAGCCAGTAACATGTACTTTAAATTTTCCAATCAAGTC
ACTGTATTATAATGACTGTTAAGTACAGGTTTTTATTATGCTTCCATATA
ACGGCTAATGACTTTCATTTTGCCATGTGCATATTTCAGGAAGTGTCAAC
TGAAGGTCGATCTTGGATATATACATTTGCAGCTTGTGCATCAGCATTGC
TCCTGTTTCTAAGATAACGACAGATATTACATTTTCCGGACCCCGATTTT
GTTAATACCAGAATAGAATCCAGAGATTTCCATAGCTCAGCTTGGCGCCA
CCATATATGTTATGTCTATATGAACACCTCTATATTCCATATATATATTT
ATGATCGGGTACCAGTGTATGCCACATTTTAAGTTACTTCAAAGAGTTAA
ATCTTGGTCAGAACAACTGTACTTCAAAGTGCTGCTTTTATAGTGAGGCA
CCAAGTTTATGCATCAATAAAGTTTTGATCAATTTGTATCTGAGCAAA