| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017397457.1, is a part of gene, LOC108223288. |
| The genetic_marker, MK007720 TP136691, is located in gene, LOC108223288. |
| The genetic_marker, MK003684 K1128, is located in gene, LOC108223288. |
| The genetic_marker, MK009606 5_11329307, is located in gene, LOC108223288. |
| 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_017397457.1 | XM_017397457.1 | mRNA | DCARv2_Chr5:11325261..11331476 |
TTTTCAGTTGCAAACCAAATGGGAGGGAGTAAGAAACACTGGAAAATTCT
ATCCATGAGGTTTCAGCAATAGATATCACTGTGCCCATGTCCATGTCTTC
TTCTTCTCCCCCACTTTGGTTATTTTCATGCCCTTCATTTTCTTCCACTT
GTAATCTCTCATCTCTCTGCATTCTTTATCATAATCCTCAGACCATTTCC
TTAAGAAGTTTTAACATTTCAAGGTTTAGACTTTTTTGTTCCCATCAAAC
ACTTGAATTGGATACCCAAAATGTTAAGAAAAAGAGAAAACCCAGACCCA
GTTTCTTGGAACAAATTGAAGATAAATGGTCTGTGAAAACCCCTTGTTTG
ACCCAAAAATTCCCATGGGAAGAAGATGGTCATAAGAAAGGAAGTACTCA
ACAATTGCCTGAATTTGCTGCAACTGAGTCAAGAATTGATGATAACTCGG
TGGTGAGTGAGTCAGTCAGTGTTGGATTTGTGAAAAATAGAGTGAAGTTA
GCTCAGTGGAATCAAAGAAGCAAAACCCACAAAACCCATATGGATTTTGA
AGCTGAAGAAAGTAGTGGTGTTAGAGGCAAAAGGGATGGTGAATTTGCTG
GGACTGAGTCAAGAGTTGATGATAACTCGGTGGTGAGTGATTCAAGTAGT
GTTAGTTATGTGAATAGACAGGCAAGGTTATCTCCTTGGGATCAAAGAAT
CAAACCCAAGAAGGCCCAAATTGATTTAAATGGTACAAGTGTAGAAAGTA
GTAGTGTTAGAGGCCAAACGATTGATGAATTTGCTGGGATTAAGTCGAGA
ATCGATAATAATATGTTGGTGAGTGACTCAGTGGATGTGGGTAATCAGGT
AAAGTTTGCTCCTTGGGATCAAAGAAGCAATTCCAACGAGGGCCAAATCG
ATTATGAAGCTGGAAATCTAGAAACTAGTACTGTTAGGGAAAAGACGGTT
GACGAGTTTCCACAGGGTTATCTTCTACAATCGAAGAATTTAGGTATTGT
TCTCGAGAAAGATGATACCGTTGAAGAAACTGATAATGTGGATGATGCAA
TTTCAAGTGAGTTACTATTGGAGAAAAATGACAGGAAATTTGATAAGCTT
GATGAAAAGTTATCTTACGAAGGGATATTATCTGGTATTATCCAGCAAGA
AGTTGGAAGGGCTGGGGATTCTATAGATGGATGTGATATAATGGGGCCAT
TGGATGATAAATTAGGAGAAGAAGATAAACTGAAGAAGATGATGCCTTGG
GAGCCTATGGAATCTACGAAGGAGGAGTCTATGAAGAGCAATACAATGTT
GGCTGAAAAACTAATTCCGGAACCTGAACTGAAGAGGCTAAGAAATGTGT
CATTAAGGATGGTAGAGAGGATCAAAGTTGGAGCAGCTGGCATCACGCAG
GCCCTAGTTGACTCTATACATGAGAAGTGGAAAGTTGACGAGGTTGTTAA
ATTGAAATTTGAAGGACCTACTGCTGTAAACATGAAGAGGAGCCATGATA
TCTTGGAGGTTGGTTTTATAATGCTCCTGAACTTGACACGCCTAAATTTT
ATGGCCACCCATTATTAAATTTCAGCAACATGTTGTTGATATATATATCA
CTTGTATTGGTAATTTTATGAATGAACTAAATTGCACTATCTGATGATTC
TGCTATATGATTAGTATGTTGTGTGATCAGTAAAATGTAGCTAGTAGGCA
AGAGTTTTTAACAATGTCTTTTCCAGTGTTATGATTACACTTGTTTGTGA
TTTCAAAGATATCTCACTTTAAGAGAGTTTTTAAATTCTAAACTTGCTGG
CTTTGAGAATGTTCAATATTTTAACATGTTGGTTTCTTAATCTCAGCGAA
GAACTGGAGGTTTGGTGATATGGAGGTCAGGTAGTTCAATAGTTTTGTTT
AGAGGAATGGCCTACAAGCTTCAGTGTGTCAAATTATTCACCAATAATCA
GCCTAATGTTAAAGTATCACAGCCTCCAAAGTATTTCGAAGATGATTCTC
CAAATGTTACTCCCAGCAGCTCAGGTAGTTCTTCAGAGGCATCAACACCC
AATTCAGCAAGTTACACAAAGGGTCTTTCTGAAGGTGGTAACATGGATCT
AAGTGAGTTGAACTTTCTGTTAGACGAGATTGGTCCAAGGTATGTAGATT
GGGCAGGCCGTGATCCGCTGCCTGTTGATGCTGACTTACTTCCAAATGTA
GTTTCTGGTTATAAGCGTCCATTCAGACTTCTTCCATACGGGATACGACA
TTCTTTGAAAGACAGGGAGATGACTTATATCCGCAGGGCTGCCAGGAATA
TGCCTCCACATTTTGCCCTGGGTATGTGGAAAATGAATGTTAATTATTCA
CACCTAAAAATATGTAATCACCTCTGTTGTCATTCTTACATTCTATAGGA
CGAAATAGAGAGCTGCAAGGCCTGGCTAAGGCTATGGTGAAGCTGTGGGA
AAAAAGCGCCATTGCTAAGATAGCTATCAAGCGCGGTGTGCATAATACTC
GCAATGAAAGGATGGCTGAAGAACTCAAGGTAAACATACCATTTTGTTGT
GCATAACTGCATATGCCTGTGGTTCTTTGTTCTGTTTATCATGCATGCAC
ATCTGGTGTTTGCTTCAGAGTTGTGAATGTTTTGTATCATTCTAGATTTA
GTTCCTAATTTCTATGGTTAGAAACACTTTATTCACAAGCTATATTGCAA
CATACAAAACTGTGTCAAAGATAAGGTGGACTGCTATTATATATTATGGT
ATACTTCAGAAACATTGACTTTTGTAACTTATCAATTTGGTAAAGATCTA
TTTGGAAAGATATTGTTCTATGCCTCAATGAAACTACTAATTATGTATAT
GTATATGTTTTACACCGTCTATTAATAAGTGAAACGCTGCTTTAGTGCAT
CAGAAATATCAAATAAAAAGTTTTATATCTAAACAACAATAATTTAAATA
AGTATATTAAAAAGATGATAATGTAATCAAATAAAAAGACATTATATTTC
GAAAAAATAATATATTTAAACGAATTTTCTATGGTGTGCCCAAGGGCACA
CAATAGTCACCAACTCTCATGAAAATTCTAACTTTTGATTGGTGGATAGA
TAATAAATGTAAATGGCCCCCCTGCATTCACATCAATTCCACCAATCTAA
ACAAGCCATTTTCATGAAATTTGGTGCTTATTGTGTGCCCTTGGGCACAC
ATTAGAAAGACCGATATTTAAAATATTTATTTAAACCCGTGCTATGTGAT
TCTCGGACTCTCTAGAAAACCCATCCGTACCCGTGTCTAGAGGACACAAC
ACTAACACCGGGATCCGGATCTGGACGTCATCCAAAAATCAGCCTCTCCA
TCTTAGACAACCTATCTTTAATTTTAGTGACCTATCTCTAAGAGGAAGAT
AGGAATAAGAACATATATGAAGAAACATAGGTGAAATGGATGTAAAAGGA
GAAAAGAAGCAACTCTTGCAATTGTTTGTTATGCAGTATAATAGAATGAT
AGTTATTTATTTATAAGAATAATTTAAAATAATAATGCAGTGTCCAAATC
CAAGTGTCGTATCCTTATAATCCCCAAGTCTTTAATTTTGTAGTTCAAAA
GATCTGACAACCTGATATGTGTTTGTTTCGGATCCTTCTAAAAGAGTCTG
AGCATCATAGTCCGTGCTTGGCACGGGTCATAAGCTAATGTTCAAGTACA
ACAAAAATACTTGCTTTCTTATAAATATAAACCCGTGTTACATACATTTA
GGATCTTGATGCTTGCATCCGCAATACTGAGATGTGATCCAGATTACCCT
AATGTTTTAATATATTGTATCCGGTTTTACATTCTTTCAGCTCATACAAA
TTTATATCATTTGTGCAGATATTAACTGGGGGAACACTGATATCTAGAAA
CAAGGACTATATTGTCTTTTACAGGGGTAATGACTTCTTACCCCCTGATG
TAACACAGACGCTGGTAAAAGCGCAAAACCTAGCTGCTATCAACCAGGAA
GAGGAAGATCGGGCCCGTCAAAAAGCGTTTGATCTTATGGAATCAAATAC
CAAAGCTTCTAAGGAACACCCGCTGGTTGCAGGAACGCTTGCCGAGACCA
TGGCAGCAACCTCACGCTGGGGAAACCAGCCAACCGCTGAAGAAAAAGAG
AAGATGATGAAAGACTTAGCTTTGGCTAGACATGCTTCTCTAGTTAGGTT
TCTTGAGAAGAAGCTTTCCCTTGTAAGTATCAAATACACTAGTACGAGTG
TTCCTTTCGTTACCTGTAAATTACATCGAAACATCACTCCATATATGACG
TTTAATGTGCTATAATAATTCAGGCAAACAGGAAAGTGAAAAGGGCTGAG
AAGGCTTTACGAAAGGTGCTGGATTATCTGGAACCAGCTTCACTCCCTGA
TGATCTGGAAACTTTAAGTGACGAGGAAAGATTTCTATTTCGTAAGATTG
GCCTGAGTATGAAGCCTTTTTTGCATTTAGGTAATCACTCCCACTTTCGT
AGTATCCTTCTGATATATAATAAGAGCTGAGATTAATATTATATGGTTTT
TTTAGGGTTAAGAGGAATTTTTGACGGCACCATTGAAAATATGCACTTGC
ACTGGAAGTATCGCGAGCTGGTAAAGATAATAGTTGATGGTAAAAGATTT
GCTCAAGTCAAGCATATTGCTATTGCTCTCGAGGCAGAAAGTGGTGGAGT
ATTAGTATCTGTGGACAGAACTACTAAAGGCTATGCAATTATAGTTTATC
GTGGAAAAAATTATAGGCGACCCAGTGCCGTGAGACCCAAGAATCTTCTT
ACCAGAAGGCAGGCTTTAGCTCGATCAATTGAACTTCAGAGACGTGAGGT
AATAGAAATCTGAATCCTATGTCAAAGAAGAGGTTCTTCCTCTCAAAATA
TAAAAATTTTGCAATCGGACTGAATATTAAGAGGGAACATTTTTACCTGC
ATTCTTTATATCTCAATTAATTATGTTCTGGGGTGTTGGTCTATTTCTGA
TCTATGTCCAAACATTTTCAGGCACTAAAGCATCATATTACAGAGTTACA
AGCAAAGATTAAGAAACTCAAGCTTGAGCTGGTTTGTTTTCTCCTCACAA
TTAACATGCTAAGACAGACAAATATAAAGAAGCTCTTAACTTATTATAAC
ATACTTTTTATGGACTTCTGTTATAAAATTTGCAGGAGGATATGACAGTC
GTAAACAGGATTAGTGAGGATACCTTTTACTCAAGGGTAGATAATGCTTC
TGACAGTGATGAAGATGATGACGACAGCATGCAGGAGGTAAATATAACTG
ATATTTTGCTTGCTTAAACATATTTTTCCTCAATGAAAGAACATTATGTT
GTGTCTGGTTAGGGTGATTGGAATGAGTGAAAATGAAAGGAAATAATTGA
GGGTAGAAGGGAGGACTTGAAAAAAATGAGTGGATGCAAATTTTGTGTGA
TAAGACTTGGGTAGAAAATAGGTATGATAAGGAATGGAGCTTTGCTCCAT
AAAGTGGAAGGCTTGAGCTCTCGTTAAGGTTGATAGGAATGGAATGGTGG
AGGGAATGAATTTATTAAACATTTAACTAAATTATAGTTCAAATTCATTC
ATTGCCTCCATTTTCATTCTACCCCAACCAAACACAACATTAGTTTCTGT
TTTAATCCTTAAAATATCAAAGAATGTGGACTCTATAATTGGACTCTCAA
GCTCTAATTTTTCCTGCAGTAGCTAAGCATCATTCTAGAGCAGTGATGAT
CAGTTCTGCTGATTTTTAGACTATTTAGCCCAAAAAGGTCTGCTAGATCA
ACCTTGATCGACATGATATTGGTTTTGTTTCTATGGTGCAGGACGACGAT
GAAGAAGCGTACCTTGAAGTGTATGACAGCGGAGATGAGGATGGTAAATC
TGAAATGGCATTTGGACATTGATGAGAGCAAGAAAAAGATGCATTCTCCT
AGATATTCATGATGTACTAGAATCCTTGTGCCCATATTATGGTTAGTCAT
CTGAATATATTTACCAGGCCTCGGCATGCATATTGTGATAATTCCTTTCT
TATGTTAGTGTACGGCCAAATTTAGATCTACCTGAAATAATGTTAGTCTC
GAGCTTGTAAAGAAAAATAGCAGCAGTATATCTTCTTTGATTTGAGTTGC
GTGTATATTGTGTAATTTACTTATTTGTTCTTTTTGTGGCAATGCATCAG
TAATATTTGCAGCCA