| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017401350.1, is a part of gene, LOC108226396. |
| The genetic_marker, MK003433 K0877, is located in gene, LOC108226396. |
| The mRNA, XM_017401349.1, is a part of gene, LOC108226396. |
| 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_017401350.1 | XM_017401350.1 | mRNA | DCARv2_Chr6:26546289..26552244 |
| XM_017401349.1 | XM_017401349.1 | mRNA | DCARv2_Chr6:26546289..26552244 |
CAATATGTGTGGAAAGTGGGATTCATGTACAGTACAGCCGTATAGGAGAG
GAGGTGGGCATGTGAGGGTTAAAGTATCTATACTATTCCCATCTCTCTCT
CTCTCTCTCTCTCGTTTATATCGACTTCTCCGCCGTGTGAATCTCGCCGT
CGCCGACTTGCAGGAGTATTCTAGATTCCAGATCTTTAGTGGTAAGGTTT
CTCACTCCTGAACATTTTTTCATCTCTACCTTCTACCAATTCAATCAAAA
CACTCGATCCTTCTCAATTCAACTCTTAACCGTTGTTATGTTCTCAGTAG
AGTGCTTAACATCACTCTTAAGATCTAATACATTTGCTCGTCGATGACGA
TTTTGTTTTTATTTTAGTAAACTTTTAGTCTTATATATTTTGGACTGTAA
CTTTGCCTTAATTCTAAGTTTGCGATTTTGCTCGAGAATCTGTAGTATAT
TGCATTGTTTAGAATTTGTTAATATGTTTTAGGGTTTTGTATGTATGGCC
GCTTAGGAGAGGAGAGCTGGTGGCTAGGGTTTTAATATAAGGGTTGAGAG
GACTAGTTCAGCTGTCTGGCCGAGATTTTAATGTTCAAAATAGCAACTGT
ACTGTACGGAGATAAACCAGTAGTGTAATTGATCAAGCAATGTAGTACTG
CATTCTGGACTATATTAGCAAGTTGGGATTGACAGTTTTTTTTACGGTGT
GACTAGTTACTTTGTTGGAAGGATTAGACATTAGATTTCACTCGAGGCTG
TCTTATTATTTGACTGATTGTAGAGGCATTTGTGTCTTGGAATGATAATA
CTTCCATAATTGATTGTCTAGTGCTGGTGCATGACTTGACTATAAGTAGA
GAGGTTTGCAGAAATAAGGAAGAGAAAGAAGGATGTAAACAAATTCTCAC
AATAAACCAAAAGGAATCTAATTCAAGAGCTTAGAATTGTTAGCAAGGCC
GGCTTTATTGCCCTCCCTGCACCAAATTGTAGACTATTGAATTATGGGCT
AAACTAGTATTATTTTGCTTTGAATCTGTATATAATAGCAAATAAGGAAT
TGCTAGCTAGACCTGCTCTATTACCATCTCTGGACAAAGTTGTACATTGT
TTAACAAAGCAGTTGTTATTTATCTTTGCATTTTTAAACTTACATAATAG
TTCCTATAAAAAGTACTATATATATAAATTAAATGTCTTAGTTCTTGTAT
AGGTAATGGCTACGGACTCTAAGAAAGACCAGAAAGAAGTTGCAGAGATC
GCAGGAGATCTTTCAGCTACAGCTTCAGAGGAGAAAACGATGAAAAAGAA
GAAAAGGGGAATTCTTTCTCGAATATGGAACTGGGTATTTAGGTTACACG
GTGATGACTTTGAGAAAAGACTGCAGCATATTTCCAAGGAAGAGGCTGCT
ATTGTTGCTAGATTAAAAAGGCGATCTATAAATCGGAGGGGGGTGACCAA
GTATCTTATTATTTTTTCTGTACTTCTTGAGGTAATATTTTATTGCTATT
GCGCTTCACTGCTTTTACTCGGGTAACAAAATCTGCCTAGAATCTCGTAA
AGAATTATATCTTAGAGTTGCTTGCAGTCAGTTAGTCCAAAATAGTTCTC
ATACCCTTACAGCGCTAATGGGACTTATGTATACTTGCCCACACGATGTA
ATGAATTTAATATCGGATTATAATGTGTGATTAGCTGGTTAAAAAGGGTT
GCATAAGGCTCACACATTAGCAGGGTAGGAAAGGAGTTGATGTGTGCAAT
TATGCAGGCTTACCCAATATCTTTTAGAAAGAGGTTGTTCCTAAGGTTTG
AACCTATGACCTAGTGGATAACAACTATAAAGTGCGATAATTTGTTTTTA
TTTTCAAAAGGGTAGGAGCTTTAGAAGAGTCGTTAAAAGTTTGTGCGACC
GTGACGAAGAATAGACCCTTTTGCACTTGAGGAATATGTTTCATCCCAAA
GCTGAATAACTTTCTGAAAATGAAGGATTTATTATATATATGCCTACAGT
TGGTGCATAATTCTATTAGAGCATAGTGCCAGTCACACAAGTTACAAAAG
TCAAACTATAAATGTTGATATATATAAAAAGTTATTTATGAACGTAAATG
GGAAAATTAAAATTATTAAAATGGCTAACTTGTAAATTCAGCCAATACAT
ACTTTCTAATCGCAACTATGAATAATATTGATTATTTTGATGCTTTTATT
ATGTGTGTATAATGTATTTACATAGGGAGGCTTAAGTTGCAAAAAAATGT
TATAATCATTAATATGTATGTGAGAAAGAGACATACCTCACCTGCACCTG
GCTCCTTGGCTAACACATTGAAGTGTGGGGAAGATGTCACACAGTGCCTA
GGCCTTTGATAACACTGAGAGCGTCCAGGGGTTCTATTAAACGATCATAC
GCATTGTAGCTAAATGATAATGCGTTTGTATACATGTACCATGTATGTTC
TTGATTTCTGCCTCCACCACTAATGAAGAGAAAAAGTTTCACAAGCTGGA
TGTAGGTAGGCCATTTAGAATCTAAGATACCCTTAAGAGTAGGCAGTATT
AACAGTAAGACAATAATTAATATTGAATAATAATGTTTAGCCTATTTTTG
TGAAATACATGGAGTATTATGCATATCTTAATGCATGTATTTGTTGCAAA
CAATGTAGAGCATATGAACTTCATATTTGTCACTAAATTATAGATTCGTT
TTTGTGTCATTCAGCATTCACATAGTCCTATACTGTCTATTAACATTTAA
CACCATTAAACAGACCTCTAAGCTGAAATGCTTAGGTGAGCCACATATTC
GAATATCGCAGAAGAAGTTTGTTTGAAACAATTTTCTGTTACGTGTATAA
GCATTTGGTGGAGAAGATAGTTCTTGCTTAGCAGTTTGTACCTGTTTATC
TTGATCCCCCCTGTTTCCAGTTATTTGCAGTGTGTTATGCTATCATGACA
ACAAGGTCATTGGATTTGAACTGGAAGATGAGAGCGCTACGTGTGTCACC
TATGTTTCTCTTGCCTGTTCTGTCGTCACTCTCTTATTCAGCTATTGTAA
GCTTCACAAGGATGCGTAAGTAGTTTAACTTTCTCTTCCCATTAAATATT
ATTTTTATCCTATTTTCATATTTTGATAGTACTGATTGAGAGTTCAGTGT
TGACTTATCTTCTATCTAGGTCGTAAATTGTGATACTGATTTCATTCTAC
ATGCCTACTGTTTATCTTGCATGAGGTTTATCAGTATGTTTTGCTCGAGT
ACTTTACTCCAAAAGAACCCTGAGCCAGTAGGCTTTATCTTTTAAAACTA
CCACTAGGCGTACACTGAAAAAATCGATTAGGAAGAAAGAATGACATACA
TATAGGTCAACAATTAAGGAATATATGGACCCAAGGAAGAAGTATTGTTT
CTTTCTCTCCTTGTTGAGGACATAATTAGTTAATTACATGAAAGACTTTT
GCCATGCATGCCATGATGGTTGGTGAGGCAAAAATACACATACAGTTTGT
TCAGCTGCAAGCATTTCTCTGCCAAGTTAAAGACAATTAGAAAGTATCTA
TTGGATGTTGTGGCTCATTGTATGCTGTGTTTACGGGTAATTGATTCTGG
TAGCAGTTATTAAAGTGATCTCTTTCCTTCAGTTATATACTGCACGAAGA
TTGCCACTTTTTTTTAGTCATGAAGTGTGCCCTTTTGAAAGTCAATGGAC
TTTCATGTTAGCTTAATTCATGCTGTATGGTTTTTAATTTGTCATCGTAA
ACCAAGCTGCAAGAGTCAGCTGCCTTCTGTTTCTCAGTCTTAAGTTAGTG
GGCATGGTGTCAGCTGGAATTATTTATATAGTTTTTTGGGGTCTTTATTA
TCTCCATCATTAGGACTTCTGGAAAAGATTTATTGAGTAAATATTCATGA
GTTTATGTAATGAGGTTATGCAATCCTTTCATGTTTGAAATTTTTTTGGA
TGGAAAATTATAGAATACTAGAATTTTTTTAAATGAAAATGATGGTCTTA
CTGATTAGCGTTCGATTGTTGTGATTTTACAGGTGATCGTAAGGATCAGA
AAACTTTAGAAAGGCTTCGGGCTGAACGACTAGAAAAAATAAATGAACTT
AAAGAGAAGACGAACTATTATATTACGCAACAACTTATTCAGGTAATGAC
CATCTTGTGTTGACTGTTGTACATTTTCTTGAAGCTTTGCGAACTTTCCG
GTTTTGTTGTTGTATAGAAGTTAAGCAAGTCCAATAGATCAGCTATGTAG
TCTCATAAGTTAAATTTAATCAATGAGAGTAAAAATGGTGCTCCAACAAT
GTCCTAGTGATACCCCTCCAACAATGTCCTAATGATACCCCAAATCACCC
GGAGACTCCTTTACTATAAGGAACCCATCTCTTCTAAGGTCATCTTAACT
TAGATTTTATAATAATCTATTACAAACACTCTCTTTCTGTCTCTATTGTG
TATTGTTAGAAAGTACTTATAATGAAAATATTGAATATGGAATGAGGATA
ACATTGTTGGAGTTGAAACTACCTATCCAGGTCCCAAGTTACTGGGATCT
AATTTATATAATATATGCAAGGAATGAGTTAGGATACTGTTGGGCTTGCT
CTTAAATGCCTATTGGTAGGTCAAAGAATCACAACTTGACTCGGAATTGA
ACAAATAATTTCTAGACTTATCATGAAGGGGGGGAAAAGCATTAAGCATA
CAATTACTCTAATTTTTTACTGCAGCATTTTGTAACTTGACTTAAATGAT
GGGGAAATATAATACTTGCCCTAATAATTGAGAAAATATAATGTATGTAA
ACCACATTATGTTTTTTTTTCAGAGATATGATCCTGATCCCGCAGCAAAG
GCAGCTGCTGCAACTATCCTTGCTTCCAAGTTGGGTGCAGATTCTGGCTT
GAAACTGTATATGGGGGATGACTCAAAGTTAAATCCCTCAACAGGGAAGA
GCAGTGATGTTGAAAATGTGCAATCTAGTGGTCTAAGAAATCGCAAGCAA
CAACTCTCTAGATCCAGTAGCGGTTCAAGTGCTGTAATGCAACAGTTAGA
AGGGGAAATGATGCAACATGCTGCAACTGAGGGATCTGATATGGCTAGAC
ATGACCAGATGGTTGTTGAACATGAAAATCCTACAAGTTTGCATGCGCAG
GACGGCGGATGGATTGCTCGAATTGCAGCTTTGCTTGTAGGAGAGGATCC
AACTCAATCTTATGCACTTATATGTGGCAACTGCCATATGCATAATGGTG
AGTAGAGTAAAATTACAGGACTAAAGTCTTTTTTTTATTCAAACAAGTAC
ACTTGATTAATGATGGAAATTATATTCTCAGGAAATATATTATACTTAAT
GTTACTTGCATACAGGGCTTGCAAGGAAGGAAGATTACCCATACATAACT
TACTATTGCCCACACTGCAATGCCTTGAATAGGCCAAAACAACTGGAAGG
CAGTTCCCCTCCAGGTAGTTCACTGGTCAGTTCCCCTATATCTGGGCCTT
TAAAACCGGTGGATGAAGTTAGTGTGGACCAAAATGTTAGTAAACCCACG
AGTGACAGAGCATCTGATAGCAGTAGCCCTGTGGCAGCTGCAGTTGAGAA
CAGAGAAGCAACCGAGACGAGAGTGTGTGAGGGTGAAGTAAGCTGATTGC
TGGTTTTTATGGAAGAGGATACCATTAGGCGCTTGCCTTTACAGTTGGTA
GAGCCAAGCCATGTCAAGTATTGTGATTGTGACGGTTTGCTTGGGGTTTG
TAGCAAAGATATGGTTCTATATATAAAATATACACATAGCAGAACTCTTG
GAATAGATTGCACAGCTTTACCTGAATATTTGTAAAAGTAGCTTTGGTTT
CCTTGGCGTAAGCATTTACTGAAATTCCCCTGTTGTGAATTTGTATGAGG
TATTGAGGTTTTATTTATCACAATTTTGAGATTAGAAGTATCAGTTAAAT
TGACA