| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017393655.1, is a part of gene, LOC108220021. |
| The genetic_marker, MK000045 CHXE, is located in gene, LOC108220021. |
| The genetic_marker, MK002640 K0104, is located in gene, LOC108220021. |
| 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_017393655.1 | XM_017393655.1 | mRNA | DCARv2_Chr5:22110481..22116754 |
CTAACGGAACAAAACAAAATCAACAAAAAGTTTGAGTTACCAAACTCCCA
AACATGCCTTACCATTCTATCTCATCTCTCTCGCTCCTCCCCATTCCTAT
CCGCCAAAACTTGTCCAAACACCACCCACCATTTCATCAACCACCTCACT
CACTCCCACTCTCCATCAAATCTTCACTCGACAACAAGCCACCCAAGTCC
AACCAAGGCTCATGGGTCAGCCCAGACTGGCTCACTTCTCTTACCAAGTC
TCTCACTCTCAGCAAAGATGATTCCAACATACCCATTGCCAGTGCAAAGC
TTGAAGACGTGTCTGAGCTTCTTGGGGGTGCTCTTTTCTTGCCATTGTTT
AAGTGGATGAATATGTATGGGCCCATTTATAGGCTTGCTGCTGGGCCGAG
AGATTTTGTGGTGGTCAGTGATCCAGCTATTGCTAAACATGTTTTGAGGA
ATTATGGCAAGTATGCTAAAGGTCTTGTTGCTGAGGTTTCTGAGTTCTTG
TTTGGCTCTGGCTTTGCCATTGCTGAAGGCCCTCTTTGGACGGTAATTTT
TTATGCTCTATTATATTTGCATTTTCACCCTTTTGGATTTTTTTGCTAAC
TGCTTGATTAGAATATTTTAATTTCGTGTTGACTTTATTGTATGTTTGTA
GCATTTCTATCGTGCATTTCCTCTACAATTGATAATTGAGACTTTGTTAT
AGCATTTATGTAATAATCCGGTAGATGCGGAACTAGAAATTCAGGAGAAA
TAGGAGGGAATGTTTGTAACAAGTGTCTTAATATCAAGAGAAATAGTTTA
ATACATGGGTTATCATGTAACTTTTGATTATTTTTGAGGTCTGTGGACAC
AATAAGAGTTTTAGAACCTGGGAACAATGTGACTGGTATAAGTATGAGAA
CTTTGGAAACTACGAGGAAGAATGAAAATTTTGAAAACATTGAAGAAGAT
ATGTAGCTAAAAAGGAGATGAGGGCTTCAGCAAGGGGTGGATGCACAAGG
GGGAAGGTAGTCGCGGCATATTATTTTGACAGAAATTTAAGCATACACCA
TTTGCTAGATTTAAGTAATGCTGTGGGTTTGAATATTACAAAATGAAAAT
CGTCGTTTCTTATCATATATTTATCTTCCAGAGTTGGCTTTTATCTAATT
TTGTAGACTCGTACCAACTTCAAAAATGGTCTGGGGTTGCAATATACTAC
TGTAATAAATCATTGTATACTAATTTATTTTTATAGGAATATCAGCACAT
TTGCGAAATAGAAATATACCTCCACTGTCTTGAATTTTTGAATTTCCCGT
TGTTTACAACTAGCTCAAGTTGCGTTAACGTGTGGGTGGGAGTTGTTTTC
CTCCTCATCCTAAACCTGAAAATAGTGTTACATAATAGGCACTAAAGAAA
TCATTAACCCTATTTGGCAATTAGCAGATTTAATTATGTGTTTTGACTAG
CTGGAGTAGCTGCTTTGCTTTGACCAACGGATTGAATTCGTTGTTTTGTA
TGAGACTGTTTGGTACATAGTTGTCTGATTAGCTTTTTGTATATTAAGTA
GACAGTTGACACATGACAATCCTCTAATTAAAAAAAGTTCCACCAAATTA
GTTTTTTGAGTCCAAACCGGTATTGCAGTCTGCTAACTACCAAACACCAA
TATTAGACGATTTACATGGTAAAACCTCTAATTTCTTCTTATAAACCTCT
AACTTTCAAACAGGGCCATAATAAAGAAATTAACTTAAGTATCTGGGTAC
ATTATTGCCATAACATTCTGTGTAATTAGAGAGTCTTCCATACAAAAAGT
CACTTGACTTGTCAATATCTACCGATGATAAGTTTTTTTATTGCTTTATG
TTGAAACTTTTAATTCTCCTGGTGCCATTATAATATAAGACCAACTTTAG
CCAAGATGCTTATGTTTAGTAGAGCTTCAATATTTTTCCATTTTTTAAGC
AGCAAGAATTTTAAGGTTGCCATTGAACTACAACACCACATGCTCATTGT
ATACATTGATTACAACACATACTATCACAACTGGAAATACTCATCTTTAA
GTACATAATATGTAAACTTACATCATTTTTTTTTCTTTTTAATTATTCGA
ATTCACTGATTGACATACATGTGGTTATGTTGCATTTGTTAAATGCTCTA
TTACGGTGTCACAAAAAAGAAAATAGATACTGAGAACAAACCAACCAAAG
CAACATTTGTAAAATGCAACATGACCACTAAGTATAGGCTATCAATCCCA
GAAATAAAGTAACTGGAGAAATTTTTTAAGACAAGCTTACATGTCACATG
TTAAATAATAGAGTAAACTTCAAAGTTGTGGCCAAAGTTTACACCGATTT
TTAAAAAGTTGGCCAGAGTTCCAAATTCTCAAAAAGATGACCAAACTTTG
GCTCCGCTTTTTAAAAGTGTGGCTCCCGTTAAATGTCACTAACGGAAGCC
TAACGGAAGCCACATTTTTGAAAAGCGGACCAAAGTTTGGCCACTTTTCT
GAGAATTTGGAACCAATAGAAGGGTAAAAATGAGTTTCAAATTCTCAAAA
AAGTGGCCAAACTTTGGTCCGCTTTTAAAAAATGTGGCTCCCGTTAATGC
ATTTAACGGGAGCCACACTTTTAAAAAGTGAAGCCAAAGTTTGGCCATCT
TTTTGAGAATTTTAAACTCTGGCCAACGTTTTGAAAATCGATGTAAACTT
TGGACACAACTCTGAAGTTTACTCTAAATAATAAGTACTAATAGATATAG
TATAACTTGTGCTATGATTTAAATATATACAATGTGAATTTGTCTATGTG
GTTAGAGCTCGCCAAAGGTAGATTATGTACTTTCTATAATTATAAAGTAT
ACTTAAGTTGAGCATGTGGTATACACTTTCAGTGTAGCCATACATGCTCC
GAAATGCAAAGTTAATGGTATTTTGAACCTAGATATATTTTTAATCTCTA
ACAATTAACAAATCTAGTGTATGATAGGCGAGACGCAGGGCTGTGGTTCC
TTCGCTTCACAAGAAGTATTTGTCAGTGATGGTTGACCGGGTGTTCTGCA
AATGTGCCGAACGACTGGTGGAAAAGCTTGAAATTAGCGCATTAAATGGC
TCTGCTGTAAATATGGAGGAACAGTTTTCTCAGTTAACTCTGGATGTTAT
TGGTCTATCAGTGTTCAACTACAATTTTGATTCGCTTAATGCTGATAGTC
CTGTTATTGAAGCAGTTTACACTGCTTTAAAAGAAGCAGAGGCTCGATCA
ACTGACATATTACCATATTGGAAGGTTGATTCTTACCTCAATGGCTTTGC
TTAATCCAAATTCCGATGTGATTTGTTTTTCATTTAAAGTTAAACATGTC
TTCCTTTTTACTTCTATTGCAGATTGAAGCATTATGTAAGATTATCCCGA
GACAAGTAAAAGCTGAAAAAGCTGTTACAGTGATTAGAACAACAGTCGAA
GAACTGATCGAGAAGTGCAAGAAGATTGTGGACACTGAAGGTGAAAGGAT
TAGCGAGGAGGAGTATGTAAATGAAGCCGATCCTAGCATTCTACGGTTCC
TGCTAGCCAGCAGAGAAGAGGTAAACACTTTCAATTTTTTCAGCCTGATA
AACATGTGATCTAAGATAACATCGATGTGATCTAAGCCTGACAATTACAT
TTTAATTGTCTCATATCTTATCTAAGATAATATACATGTGCTAGGTCTCA
AGCACACAGCTGCGAGATGATCTTTTATCGATGTTAGTTGCTGGCCACGA
GACCACCGGCTCTGTGTTGACATGGACATCATATCTTTTAAGTAAGGTAC
CACCACTATTTTCACATATTAGCAAAATTTGCAAGTTGGTGAACAGTCAA
ACAAAAAGAGAAGCAGTTGATTTTGGATAGAATTTGAATTCAATTAATAT
AAATGATTAATTCGTATCTAGCTTAATTAACTTTCAAGTTTTAACCAACA
AAGTATCACTTATGCATACATAATACATTGAACTTAACATATAAGAGTCA
AAGTGTGAAAATTTGTTTAAATCAATATCTCATCCTGATGTTATGCAAGG
AAGTCATCACTGTTGCTAATACTTACCACAATTGATAGGCGAAACCTTGA
TATTCACCCATGATGACTTGCAGCAACAGAAATAAGCTTGAGACGAAAAT
AATTTTGATAAGGGTGAATTTACATGAATGACAAGTTTTAGGGTTGAGAA
TGTTTATTTGTTTATGCCAATGGTTTATATGAGCAGACAGTGTAACTTTG
GAGGTCCAGCAGTTTAAGCCTTTGTCTCAGAACTTGGTTGCTGTAAAATA
CTTTGTCCAATTTAGTTCCATGACATGGAGTACACTACATATGCTTAATT
CTTTATAAACGTGCAAATAATCAATAAGATGCTAATGCTTACTCTACTGT
TTTCCTGCTTGATACCTTTATTCAGAACCCTTCTTCTTTAGTAAAAGCCC
AAGCAGAAGTTGATAGAGTTTTAGAAGGAAGGCCTCCTACATATGATGAC
ATTAAGAATCTCAAGTACCTGACACGCTGCATAAATGAGTCGATGCGTCT
TTATCCACATCCTCCTGTAGGTTGCATCCTTTCCTTTTAGTTCAGTGAGT
GGCTGTGTAACTCTTTAAATTCATTCATTGTCCTGGATTTATCAATTTAA
GGTTCTGATTCGAAGAGCTGAAGTTGCTGATGAGCTTCCTGGGAGCTACA
AGGTTAATCCTGGGCAAGACATAATGATTTCTGTATATAATATCCATCAT
TCTTCAAAGGTAATTCTGCTCATTCCGGTTTATTACAATTACATTCCATC
TTATTATTGTCGTTTTCCTTCTGCTCATAAATTTGAAAATCTAGGTTTTA
TTACATTTTATGGGGACATTAATTTTCTCTTAAGCAATTACTACCATATA
GACGTACCATATTTTGTTTTATGATTATCTATATTTATGTGAAACCCAGG
TCTGGGACAGGGCAGAAGAGTTTATTCCGGAAAGATTTGACTTGGATGGC
CCGGTGCCAAATGAATCAAATACTGATTATAGGTATCGAGGACTCTTTCA
TCTGAATTCAGTTATACATAAGATGTACTGTTGGATTAGAGATCCGTTTA
GATATGGGCATATGGCTTACAATCTCACGCACATGTCTGTTTTCCTAAAT
TATTGGGACTCTCACATAACAATATGTACCATTGCAGATTTATCCCATTC
AGCGGAGGTCCTCGCAAATGTGTAGGTGATCAGTTTGCTTTACTGGAAGC
AATTGTGTCGCTAGCTATATTCCTGCAGCACTTGAGCTTTGAGTTGATTC
CAGATCAGGTTATCAACATGACAACAGGAGCCACTATTCACACAACGAAT
GTAATTTTCTCAATTAATAATAGTTTTTAATTTCAACTGCACACTCATGC
TCAACATTAATGTCAAAGATAGCCTGGAGAGGTGAGCTAAAAAGAGATAG
AAGCAGTTTTACTGATTACATTTGCACAAAGTACTAAGTTATAAGTTATA
ACAACGCTTCAATATAACGATCCGTTAAAACATGTTATAAATTCAGGAGG
CCCGTAGTCCCAAATCCCGAGCAACTAACTGACCAAATTTGTTAATATTT
CGGCTTTAATAGTATAGATATGTATATTGATGTACAAATTCATTTTGTTC
CCAACCACTTCCATTCCTTCTAACCAAACAAAGTGTAAAAGGAACACATA
TTACACAATGTCTTTTGTACTTATATGTAGTTGGTGATAGCAGCATAAGG
TGGTAAATTATATAGTGAACAAGAACAAAGCTAAATCTATGTTTAGTGAA
AATAATTTGCTTGCCTAATCCCTAGTCTAGTCTTTAGGAAGTTCTAATAC
CCTTTTTCAGCAGGCAGTCTTCCTTCTATATACAAGACATAAATACTTGA
GGCCACTTATTTTGCCATGACAGCGAAAAAACTAATTGTAAATCGGGTAT
GGACTTATATTATCTCTGCTTACAATCTGCCTTTTTCAGGGATTGTACAT
GAAAGTGTCCAAGCGGCAAATCAAATCAGCAGCTGTTTCCTCAATATCTA
GGTAAACTTTATAGTTCTGTACATAAAAGTGGCAATATGTTGTATAGAAT
GTGGGATGATGAAGGTGATCCACTGAGGCTTCGACTCTATTGATTTATTA
ACCGAGAAAGAAAATTCATTTAGCAGCTGAGAACAGAGGCAAGTCTTGCA
AGTTATTTGATAAAAACATAGTTGGCCTCATAAGTACTACTGTATATAAA
TATTGTTAGTGTCAATTACCTGC