| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017381723.1, is a part of gene, LOC108210440. |
| The genetic_marker, MK002796 K0240, is located in gene, LOC108210440. |
| 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_017381723.1 | XM_017381723.1 | mRNA | DCARv2_Chr3:1207017..1213969 |
TACAGAGTATATATGACTGAAAGTCTAAAACCCTGACCCGATACACTAGG
TCTAAACTACTGTTGTAATAGCTTAAATGCTTCTCTGAACTCCGGCGAAC
GGCGGCGCCACCGGTGAATTCAATTTGGTATCTCATTCTCATACTAACAT
TGCTCTTTAATTTCTAGTCTCAATCACTTTGTGTATCACTGTGTGTAAAT
GCTTGAAATGTGATGATGAAATCGCGGTATGTAATCTCGCTATTAAGTTT
GTTACGAAATGATTTGTGTGAAGTTCCCTGAGTAGTTGCTTAATTTCACC
AAATGTGGATATCGAATTTCGAAAGCTAGAGCTTATGATTTTAATATACC
TATTCTATGAGGGTTTATGGTTTTAATTCACATTTGTGGAGGTAAGTAAT
GCCACTAATTAATCTATTGAAGGCGGTTCTTGTGTGCGTCGTATAAATGT
GGTGGAGTTTATATCAGTGTTCGTAGTTTATTAATCTGAAATGCCCTGAT
CTGTTGCTTAATTCCAAGAAAGTGCGAATATCAAAACTCGAGTTCTAGGG
TTTATAGTTTCGCTATACATAACGCTAGGGGTGATTATATTTAATTAATG
TGAAAATACATATGTTGAGGTGAATTATGCAACTAATTAATTTATTGATA
TCTTTTATGTATCGTTCGACTGGATGTCATGGTGGAGTTTATATCAGTAT
TTCTAGAAATTACATATGTCTACATGTTAATGGTTGGTAGTCTTGTTTGT
AATGGTGTAACTAGAAAAATGTTTAGAAGTAATGTTGAAGATATTTACAT
TAAGAATAATACTTCGGTCATTGTTGTTGCAGAAATATGAGAGGAGTTTC
GTATGTTTTGTCATGTTCTCGGCACGTTCGAAGTACGCAGTTATGTAGAC
CAGTCTCTAATTTCTCGTTTCATAGACCAATAGTTACTTTTAGTTATACT
CAGTTACAGAATATGATACCCCTGGTTCCTGATTCTCTATGCGGAATGAG
GTCTTTCTGCAATAAGGCTGCGTCGATCCCACTTGCACTTCAGGCGCAAG
TGGAAAGAGAGAGGCAGAGGGAGAGAGAAGAGAGGATCCGGATGGGGTTG
GATACTGCCGATATTGATGCTGAGGATGATGAGGATTACATGGGTGTAGG
CCCGCTTATTGATAAACTTGAGAAATGGAAGATTAAACACCCTCCGAATC
CTGAGTTAGACATGATGTACGAAGAGCCTACTGACTCTGACAGCGATGAA
GATGATGACAGGTTTTCTGCTGAAGCTAATAAAAGAAGGTCTGAAGATTT
TGAAAAGAAGTTTGCGCGCCATAAAGAGCTTCTCAAAAGTTTCACGGACT
CTAGTAACTTTCTGAATCCACTTCTTTTCTTTTTCTTTTTAAATGTGGTC
ATGTGCTCATGTTGTTGAACAACTGCTGTTGCTATCATTGTATTAATAAT
GTGTTGAAACTATGCGCACAACCTTTAATACTTTCAGTGAGGATCCACAT
CACGGTCCTCTACTCTGCTGTAATGATTGGTTTCTTACTTTCTTTTCCGT
GCAGAAACTCTAGATGAATCTCACGAGTGGATGAACAGACTTGACAAATT
CGAGCAGAAGCATTTCAAACTACGTCCTGAGTATATAGTTATTGGTGAAT
TAATGAACAGATTGAAGGAGGCTACCGGGAAGGATAAATTTCTTCTCCAA
CACAAATTGAACAGGGCAATGCGTTTGGTGGATTGGAAGGAAGCTAATGA
CCCAAATAATCCTGACAATTATGGTGCATTCCAGCATGCAGATGAAGCTG
CTGTTGAAAATGAGGAATTTGAAAAGGAACAATTGACTCGACGAGCTCAA
CTTAATGACGACGATGACATGGAATTTGACAGCATGAAGGAGAGGGATGA
TATACTTTTGGAGAAACTTGAAGCCATTGACAAGGAACTGGAGCAGAAGC
TTGGGGACTTGGATCATACTTTCGGAAAGAAAGGAAAGGTCCTAGAGCAG
GAGATTAGAGATCTTGCTGAAGAGAGGAACTCCTTGACTGAGCAGAAGAG
AAGGCCTCTTTACAGAAAAGTAAGTATTTTTGCTATCTTTTCAATTGTTC
ATATCCAAATATGATTTTGAGTGCCTTTTGTTTTTTTATCATTGCTTTTG
TACTAGATGGATGGATAAGATAGTATGTTGAATATGAAGCGTATGGATTC
TTTGGAACTATACGCCTTCCTTTCTCAATGTACTTACTAGGCACACTGTA
TATGCTCACATGCTTACCTTCTGTAAGTTGACATTTGATCCAGTTCAAGG
TTGCTCCTCACTGTTGTTCCATATGTATAATCTATCAGCATGAGTTGTAG
TATTAAACTTGCTAAATTGTTTTCCCTTTATGAGATTGGTTGCTGGAACC
TAGTTCATATTGGATAGTGTACCTCCTAAGGACGTATAAAGGGGGTCTGA
ATTTTGCTGAATGCAATCTTATGGGGCATTTCTAATGGTTAAGGGGAAGT
CCAATGGTGTGATATATTATAGAACCAAAAAATTAAAATCTATCATTCCA
ATGGTGTTCTATATCTTGTACTAAAATAGCACAATGCTATACTTTGTTCT
AAATGAAGAACAAAAGATAGATGGAGCTAAGCTAACTTAAATTGACACAT
CATCCCACCTCATCAGAAGTAAAACATTAGGTAAAAAAAGTAATTCTGTA
TTCAAAATAGTGGGGGTACTTGGAGAGTTGGTTAAATTTAGAACAAGATA
TAGAACCAAATATTGGACACATGTTTTATTTTAGCACAAAAAGCCACTTT
TTGATGCGAAATTATAGCAATAGCTCCATCTATTTTGGCACAAGACATGC
TCTAATTTATGTATAAAATGCTTCTTTTGAAGGCATATGTGGTAGGAAGT
AGATACAATTATAAACCAAATTTATGGTTAAGTGGGATGGTGATACTGAT
TAGGGGGTCGTTTGGTTCGCGGAGTGGTATGGGGTTGAAATGAGGTATCG
GGTTAAGGTAGTATGGATTTAAGGTATCATATTTGATATCATGTGTTTGG
TTGAGTGTTGGAATCAATATATTCAGATTTAAAAAAAAAATCAAATTATT
TCTTTATATTAATTAAAAAATCTAAAAAATATTATTATTATATGTTTTTG
CATCATTGATTATTGTTGTATTAAAAATTAATATTTAATTACTGAAATAG
AGACAAAAAATTAAAATTAAAATTAATTCCCATACTTCCATCTCATACCC
ACCTCCCCCTTTGAGCATCAAAAACCCATACTTTGAGGGTTTGAGGTATG
GGTTTAAAGTTTTATTTTTTGCAACCAAACACCAGGTATGGGTTTGGAAT
GAACAAAACCCATACCCGATTCCATAAACCCGTGAACCAAACGACCCCTC
TTTATTATTGAGAATGCCTTCAAGAATCTCATCAAACTTCAAACATGTAT
AAATGATATATAACTGTCATGGCAAGTGTTGTAAAATATTTTTTTGGATT
GTCGAGGTATGACATCATATATTACTTAGCAGTTTTAGGACACGTGACTT
GTATTTAACATCATCTCTTTACGTCATATTGGAGTGTGCATTTAAGTTTT
TTTGACATGTAACTCATTCTCATGGTTTAAGCTAGCTGACATCACAATTC
TTCAAAGTTTATTAGAAAATCCATGTGATGAAGTCGAGGATTGGCTTTTA
TACCTAGAGGAAAGAAATCACCCCTAATGTTACTGCATGATTAAAGAACA
CATAGATTTATATGGCAGGGACCATGTCTGATGCCTCTTAGTTGTTTTTG
ATTTTAGCTTTGGTCAAAACTGCTCTCAGTCTGAACTATAGTTTTGGTGA
CAAGTTTGGCTACATATTTCTCTCGGTTGTTACAACTTATGGGGTAGCCA
AACTATACTATTAGCTTATTTGGGGTGGTAGACGTGCTATACCATTCTAT
CAGCTAATAAAAAAATTATTTTAGGTATTAGTCATTAAAAGTTTTAAATC
ATGGTTTGTGTAATGTCCTCACATCTTTATTTTCACTATAGTCTTTATTA
TTTGCCTTTAACAGGCTTTCTTTGTTCTGTCCGTTATATTGTACCTGGAA
GGTTTTTTTTTTTTTGTCAGGGAAACCTGGACGGTTTAAATCAGTGTAAG
TTTACAGAAATTTAATTTGCCTCTGTCCGAAGTATATTATTGGGATAACC
GCTTTTGGGTCCTATCTCATATTTCAAGCTAAACTTAAGTCTTTCAAAGA
GTATCCCTTAAAAGCATACATAAAAGATCAAGTGATGAATTTAAAGTACT
TTTAAGTTTTAAGTGTATCTGAGTGTTTTAGTTCAAGGCCTCTTAATTTC
TTACATCAGTTGGTTATTCACATAGTTTCAGACACTGACTATTACTAAAT
GTCCAAGTTAATAAGTCTTTTGCCTTAGTTTGGGGCAGTGTTTGGTTTCA
ATTCTTGATGTCCAAATTAACCCAAGGGTCCAACTGCAAAAATAGTACTA
CTATTGAAATTTAAAATTCAGCTGGACTTGGTTTAAATTCACGATGTCCA
AATTAACCCAAGCTTACAATTGCATATTATTATAGTTCTGCTATTGAACT
TTAAAATCCAGTTGACTGTTGACAAAAGTCAAGGTAATCAAAGATTTTAA
CTTACGAGCACAACTTAGCATCCCAACTTATGGTATGGCGATTCACACTT
AAAGGTACAGGTGGGCCGCTTTAAGTAAATTGTTGATGAGAATTTTTTAG
ATGAATGCGGAGCTTCTTTTCAGATAACTGGACAGAGAGGTCAATTATAT
CTGAAAAAAGAAAAAAAGGATGTTAAATGATTTTGTTTGTCTGATTTTTT
TTTTGTTCATCTCTATTAAGGGTTACTTGAGATACCTTCTGGCGATCTCT
ATGTGCGCTATATTGAATTATTAATGGAGTATAAGTATGCTTACATGTGT
GTGTCTGTGAATATTTATTTTCACTACTGTTGCCATTGACTTTGTGAACT
TGTTGCAGGGTTTTGACGTGAAACTTATCGATGTTAGTCGAACTTGTAAA
GTCACAAAGGTAAAACTTGCTCCTCAGTCTCTTCCCATATCTAATATTTA
ATTTGCTCATTTTACAATCGCTGTTATAGGGAGGAAGAATTTTTAAATAC
ACAGCAATGTTAGCTTGCGGTAACTACAACGGCGTCATTGGTTTTGCAAA
AGCAAAAGGACCAGCAATGCCCGTTGCTGTTCAGAAGGTATGTTTTTTTT
TAATGCAGTTCATGATTTATTAGCTTACAATATAGCTACAGCAGGTTATT
GGATATTCACTATAATATGCATGGTAATTTAATCATCTTATATGTGAATA
TTAGTCCTCGTGTTGCATGTGTGCTTAATAAGAAGAGTTGATTAGGTAAT
TTGAAGGGCTTCGTTTTTCTTTCTGGTATCTATGTAGTTTTGTCATATTA
CATCTGATTAGATGCATAGAAGTGTTAATCTAATACTATGTATTTATCAA
ACTTCCAAATGACTATATGCATAAATGTTTATGTTAATTGAAATTAAGGA
ATCCACTTCTAAGTGGATGTGCACTTTAGTGTGATGTATGAGAATTGTTC
TACAGTCGCTAACCAATTTTTACAACAGGCGCATGAGAAGTGCTTTCAGA
ATCTACACTATATAGAGCGGCACGAGGAGCACACAATTGCACATGCAGTG
CAAACATCATATAAGAAAACTAAGGTGACTTATAGTTCGACACTTTTTGA
TTTTTTTTTCCTAAATTGTGAGGGAAAGCCTTTTGGTTTCATTATCGTAT
AGAAATTGCTGAACTGTCTATTTGTTACACTCTAGGTTTATCTTTGGCCC
GGCCAAACTTTGACGGGGATGAAAGCAGGCAGGATTGTACAAACTGTGTT
GAATCTAGCTGGCTTGAAAAATGTGAAATCTAAGGTATGGAATTTGAATT
GTGGCTTGATCATGTTTCTTGGCATAATGCTATTGTTTTGTAATATATAT
TTAATGTAGGTTGTTGGATCAAGGAATCCCGATAATACAGTTAAAGCTCT
TTTTAAGGCTCTAAATGCAGTAAGTACATTTAGCATAGTTTTAATTTACA
CAATTATTTGAACTCTGTAGTATCTGTTGATAATTTTTTTCTCTGCTTCA
AATTTCCAGATTGAAACCCCTAAAGATGTTCAGCAGAAGTTTGGACGGAC
TGTCGTTGAGTCATACTTGCTGTGATAGGTACGCGGGAGGCTGTTAATGG
TTTACTGATAAAGCAGTCATCAATTATTCCCCTTTGGCATTACATGATAT
TACTTCCAGTTTTTTCTTTATATGTCCTTATTAAGACCGCACCATTATTT
AAACATTTAAAGGGAGAAAACTGGCTTGCTTACTATGAAACTTTAATATA
ATCGAAGAAATCATGGTCTTAATTTTGATTAATCCTAGCAACTAAATTAT
TGAAATTTTTGAAGGGAAAGTGGAAGCCCCCATTTTTTTGGACCACGGCA
TAAAAGCCAGCTCGGAATACATAGTCAGCATACGGGGTAGAGGAGAAAGT
TTGACCTGCTGGTGACCAAATTTCATCTCTGGAATATCAAGTTTTGATGT
TTTATCTTATATATAATAAATCCCAGCTGCAACGGTCAGTAGTAATCCTA
TGTATGTCAGAAATATTCCGCCAGAGTAACTGCACAGTGCAGCTTCTTAT
CCCTTTTCTTTTAAAAATCCGTGAAGATGAGCGATATTCTTTTTACAATC
TTCACTTGTGGAATCAGGTGGCAAAAACCATCAAGAAAATGACCGTCTGG
AGTAAACTTGGCAAATTTATTATCTGAGTTAGATCCTGTTCGCTAAAAAT
AACTGCTCAGTACAGTTATTCTTAACATCATCTTACAGCATCGACGTGTG
TTGGCTGCTGGGTTTTTCTGTTAATTGAAATTAATGCATCTTTTTTTTAA
AA