| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017359415.1, is a part of gene, LOC108192890. |
| The genetic_marker, MK004458 K1902, is located in gene, LOC108192890. |
| The mRNA, XM_017359414.1, is a part of gene, LOC108192890. |
| 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_017359414.1 | XM_017359414.1 | mRNA | DCARv2_Chr6:24887721..24894067 |
| XM_017359415.1 | XM_017359415.1 | mRNA | DCARv2_Chr6:24889314..24894070 |
CGTGGAATGGTTTCAGTGATACTGACATATATAGTGTCGTACGTTGAAGA
CTAGCCATGTATGATGTATCTACCAAGAGCTCAATATGTACATGTGTTTT
TTTTCAAATAGACAAATTTATTTTCTCCTCTTCCTTCTTGATTAACAAAC
AAAGATACAATCTTTAGTGGGGGTTTCTCAAATTCCCTTTCCAACTGATG
ATCTAAAATATCCACAACACAATTTGATCTTTCTCTACCACCAAACTAAC
CAGGTCAATGCTTCCATCAAATCCGATAAGAAGCTGAAAGTTTCAATCTT
TTGAATTAAAGTTAGAGTCTTGGGTCAATTTGTATCTGCAATTGAAAGGT
TGATGTTATGATTCAGCGAATTTGAAGCAAACCCTAATAGAAAAGAAGCT
GATGCAGAAGATTATTGGGTATTATATTGATCTGTTGACTTCATCATACT
CACCACCTACATGGGCAAGTACTATTGCTGGTGCCTTTGTGCTTCTCACT
CTCACACTCTCCTTTTACCTTATATTGGAACACCTCTCTACTTACAAAAA
CCCTGAGGTATGTACTGATTGTGTGTGTGTGTGTGTGAGAATATAGAATA
TTTTTGATTTTTTTTAAAGCTTCTGATGGCTAATTTTTATTTTATTTTTG
GTTTAAATTGAATAACAGGAGCAGAAGTTTTTGATTTGTGTTATATTAAT
GGTGCCATGCTATGCAGTTGAATCAGTGAGTTTGTTTGTTAATAGGATAT
ATGTTATACTGTGAATTGCACACACTTTAGTTGTTTTCTATATGAAGAGT
TTGTGACTTTTTTATTGTTTGTTTGCACAGTTTATTTCGTTGGTGAAGCC
ATCAATTAGTGTTGACATTGGGATACTGCGGGATTGCTACGAATCATTTG
CTATGTATTGTTTTGGGAGATATCTTGTTGCTTGTTTGGGTATGACTTCT
GGTGATCTCTTCCTCGTCGTATAAATTTTAAAGTTTTTGTCAGTTTCACT
ACTGTTATGTACTTATGTTCTTAAGGTTGCTATGGTGATATATGTGTGCC
AGTGTGACTGATGAATTTAATATATAGCACTTGATCAGATTTTTTTTATT
TTTTTTTGTGAGAATTAAGATGGCAATGTCTAAGAAGCATTTCGTGTAGG
ACAATGGGTATAATGTTATCACCTGAACATGCACTCAAGCTAATTCATCG
GCACTTTTCTCTCTGATCAATGATTTATGGTTGTTTTATATTGTTTTTTG
TAATTGAGTAGGTGGGGAGGAGAGAACGATTGAGTTCATGGAGAGGGAAG
GACGTGCAAGTTTGAAAGCCCCCTTGTTAGAACACGGCTCAGAAAAGGGA
ATTTTGAAGCATGTTTTTCCTATGAATTTGTTTCTGAAGCCATGGAAATT
GGGCAAATGGGTTTACCAAGTCATCAAGTTTGGAATTGTTCAATATGTAT
GTGCTCCCTCATTTAGACAGATTTCTTGTTTATATTCTCTGACCTGGTTT
ATCGAATTATGTATTTGTTTGTCGTGATACCATAAATTCTGTGCAGATGA
TTATAAAGGCTCTCACTGCTATTTCAGCTGTAGTTCTTGAAGCTTTTGAT
CTATATTGTGAAGGTGACTTCAAGCTGAATTGTGGGTAAGGTTTTTGAAT
TGCCACCTAGAGACTAGAGTACTTTTGATTTGTGTTCATCTGTTATATAT
ATACTTTAGGAAAACACACATTTTATGCTTACCTCAGAAGGTATTGTGTT
GTTGGTGAGTTCTTTTAAAGCATTCCTTCTAAATTACTGCTGCAAGTCTG
AAGTGGGGCTTACATGAGTATGCATCTTAAAGTAGCACATGGCTATCAGC
AGGGCCGGCTCAAGAAACTTTGGGGCTCTAGGCGAATCTAAAAAATGAGG
CCTAATTTAAAAAAATAATCTAATATTATATTAATTATATAAATACAAAA
TCCTACAAAATTTAAAGTTTACAAACATAAAATCACCCTAAACACACTAC
TACAAAATTAAAATGAAACAATAACACAAAATTTACTTGCTACAAAATAG
TATTTCTACATCAGGTTTCACTAGCCTAATTCTAATATATTATTCAACTA
GAATGTGTATAATATTTTATTAATTTTATTTCTACATCAGGTTTTGACGT
AAAATATTAAATATATTTGGAATTAATAAATAAGATGTATAAATTTAAAA
AATATTAAATTTTGGAGATAATTTGATTAAATATTTTGATAAGTTCTAAT
AATGAAAGTAATTGTGTTATTAAATCTAAATTTCAATATTAAATAAACTG
AAGGGAAAACTAATTAACTATAAAATCTATAATGTTTTTTTTTGACAACA
TAAATTTATATTCACAAAAATGAGGTTACATACTTACATCCACATAAAAT
AATCATTTACATATTTATTAGGTTATAGATTCAAGTCAAGTATTTATTAA
GTTAGCACAAAAAATAAAACATGATTAATAATACTAATATTAGTATTTCA
ATTATTTTTTTGAAAAAGTTGATTACACAGACCTTTTTAATTTTTCTACA
AAATTTGAATATTAATTCTTATCTTATTTTTGAAATATTTATTTTACGAA
ACTAATAAAAAAAATTCATACTTATACTTATACATATATATATACTAGTA
TAAAACTGGGGGCCTCTCAAAACTGGGGGCCTTAGGCGGTTGCCTAAATG
GCCTGTACTATGCGCCGGGCCTGGCTATCAGTCCTGGTATTTTTTTGTGA
TATTTTAGAGCTAAATGCACTCCAGTTGACACAAAATAGGTACTCTCATG
CTTTTTGTATATTTTAGTCCCTTTCAAGGCGCAGTTACTTCACCCAGACT
TGGGTTGGTGAAACAAACAAGGGTTTGGATCCAAGATTTGGAATTGCAAA
TATGTAAATAGTAATACTTTTGAATACGGTTCTAATATTGGACATGGGTG
CAGGGACGTGGACAGGGTAGGTTAGCTCGTGATATTTCTAGAATATATAT
GTTCTTAGTTGTTTTGTACGTTTGATATTGTGTCTATTTATCATTAGATT
AAATGAACATTATGAAACATATGCAATCCATCACATCAAATTGATATGAT
AATATAAAAGCAAGTAGTCCGAAGAGTTCTAGATTGGAACCGGACTGTTG
TAAGGTTAAGAGTCTTGTTTGAGTATCATGGATCAGACTCAGATCCATAC
CCACAGTTATATTGTGTCATGTTGACACGGGTATAGGAGTTAAATTGAGG
AGTCCATCTTAGAGGGTTTTATGTTTCTCTTAATTGCTTTCTCATATACC
ATTTACCATTTTGCAGGTATCCTTACACGGCTCTGGTTTTAAATTTCAGT
CAGTCATGGGCTTTGTATTGTTTAGTTCAATTTTATGGTATTACAAAGGA
CGAATTGGCACACATCAAACCACTGGCAAAGTTTCTGACATTCAAGTCAA
TTGTGTTTTTGACATGGTGGCAAGGTGTGGCTATCTCGCTTCTTTCTACA
CTGGGTTTATTTAAAAGTCCAATAGCTCAGCAGCTGCAGTTTAAAACAAG
TGTTCAAGACTTCATCATTTGTATTGAGGTAATTAATTTGTTTCAACGTA
TACTCTCGTTCATGCGAATTTCACTTATCGCATTAAAGATATGTTATTAT
CCATGTCATTATCAGTGAAACATTACATTATTCCAGTTATTTGATAGTAG
TCTCTTTTTTTGCGTATAGATTATAGCTGATAAGTAGTACCTATTCCTTG
ATAAATCTTGGGATGAATGAAATTTGAAACCAGGACCTGGGATGACAGAG
AATTGGCTACCATTAGGTTATCCCATCACACTCAATAATAGTTAGTTACT
GCATGCACTTGTTTGTCACTACAATTAGCCGAAATGCAAAGTTGATAGTA
AATGTAATTGCCTGTGGAAAATATGGATATGTAATATTTGAAAGTCATGC
AGGGATCCTAACAAATTGTTGCTTGGTAGACTGGTAGTGAATAGTATACA
TAGGCTCCTGCATGATGGAGGGCAAATTTTTGGAGTAATTATTAACACAA
GGATAATATAGATGTCTCAACTGCCTTGGTTCACTGTTAACTGTGATAGG
AAATGTAGTGCTTTCTATATAAATGTTGCTACTTCAAAATACTGGCAGAT
TAGGGTGATGAATGATGATAATGACCTTGGCTTGTTTATGATTAAAACAA
GGTATGCAATGTTCTAAATAAAACTTATGCACTATACAGCCTACTTATAT
AATTATATATGTATATATAGCCTAAATCATGAAAACCTGTGTAAAGTAAG
GATTCTCATGTACAATGAATTAAAAAAAGACATGTGATCTAAATTATAAT
TTATTCTGGAAAGACGACCGGATATTATGCATCCTGTACCCCCCCAATCC
CCCTCTCCCTTTTTAAGGCATATAATGCTTCTGCAACATTGCTGACTAGT
TTGTGTCAAGCAGAGGATGCAGTTTTCATTTGGCCATATTATGTTTAAAA
GTTTCATTACTCTTCTGTGCCCTTCTAATAAATATGCAGCATAAAGATTA
TGTGGTCATCGTTGTAAAATAATCAAGGTTAACAGTTCTCTCTCTTCGTC
CAGAGCAGATGGGCATTGCATCTGTCGTTCACCTATATGTGTTTCCTGCA
AAGCCATACGAGTTAATGGGAGACCTCTTTCAGGGAAGTGTTTCAGTCCT
TGGAGATTATGCATCCGTTGACTGTCCTCTAGACCCTGATGAAGTGAGGG
ACAGTGAGAGGCCCACAAAATTACGACTTCCCCAACCTGACATGGGTGTC
AAAAGTGGAATGACCATCAGAGAAAGTGTTAGGGATGTCTTCCTCGGTGG
TGGTGAATATGTAAGGGATCCTGTATTTTAGCTTGTCTATATTTTAAGCT
GCCTACTTAGTAAATACTAAACTAGGTAAAATTGTGCCTTGTTCTGATAA
CTCAGACTATTTGCTTGCTGAAATTATGAAACTATTACAAAAGTAGCAAT
GGAATCGGTATGTGATATTACTTTTTTGCTCTATTTTTCCGGGGATCTAG
TTTTGCTAAAACAATTTTTGGGTAAAGTTACATTGTTGTCCATATGATAT
CGATTTCAAAAATTGAAAAACTTAGCAAAAACCCGATAATGGATGAATGC
AAGATGCAATTCATTACACTTCGCCTGTTTTATAGCTGAAATGAAATTCC
ACCAGAAGTAATCTGAGAGACTCTAGCTGAGAATCTTAGTGGGCAGAGAA
TGAGCCACTTTTTTTTTCATTAAGCAATACGTACAACAAATACCTACTTA
TTAAAGCTATTGACTACTCATAATTTTCTCATCTGTCTTTCCACCTGTAC
AAGGCTCCATCATCTTATCTTATATGTGCTTCATGACTTTTCATTTTTTT
TCCTGTCGCTTTTCTTATATTTCTTTGCAGTCATTCTTATTGCTGATAAT
GATTCTGTCTCATATGTTTTAATGTAGATTGTGAATGATCTTAAGTTCAC
AGTAAACCAAGCTGTGGAGCCCATGGAAAAGGGAATCAACAAATTCAATA
AGAAGTTACATAACATATCGGAAAATATAAAGAGGCATGACAAGAACAAG
AAAACAAGAGATGATAGTTGTATCAATTTGTCACCTCCAGCTCGGAAAGT
CATTCGTGGAATCGATGACCCCCTTCTTAATGGAAGCTTTAGTGATAGTG
GAGGATTTAAGAAAAAGAAACACCGTCGTAAAGCAGGCTATACAAGTGCT
GAAAGTGGTGGGGAGAGTAGCAGTGATCAAACGTTTGGGGGGTATCAGGT
TCGAGGCCAAAGGTGGATCACAAAAGAGTAAACATGAGGAAATAGTTAGA
AACAGTGGGGGAGAAAGAATGTTCTGCGCCGTCATTAGAAAGGTGGTATT
GTGTACTGTACATATTGTAAACATTCTTTCACCAGGCTTAGAGGCATCTG
GAATTGAATTTGCCATGATCTAGTTTTGTGGAGGAAGTTGGTGATTCTTC
TTCAATGGCATCTTGAATATCCATTTGGTATCAGATGAAGTCTGATACGA
AAAGAACCCGAGATTAAGTGTCAATATTTTCCGTTTTCCTATATATATTT
TACATATGATGGGCTTCTCAATGTTGTATAGAGTCCTCCAATGTTCTCTG
CCTGTTTTTGGACTTGTGTTACTGTGTAATACTGGTATCACAGTTTACCA
GATACATATGCTTTGGCCAACTATAAAAGAACCATAGCCTTAAATATGAA
CAGTGCAACTATTATAAGCATTGATCATGGTAACTTGGGTGTATTTTCAT
TTGTTTTCGCTGTTTATGAAGTTCAATCTAGAGATATTATCTGCTCTCA