| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017386746.1, is a part of gene, LOC108214626. |
| The genetic_marker, MK009421 1_50391326, is located in gene, LOC108214626. |
| 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_017386746.1 | XM_017386746.1 | mRNA | DCARv2_Chr1:50389293..50395417 |
GACCTGTGACCCGCCATTTGAAATTTTTTAATTAAGATTGGCGGGAACCA
ATTCTTGGTTTAGACAAACCCTAAAATCTATGCCCGGCAAATTCAGAGAT
TTCCCCGCTAAAAACTCGCACCTTTAAAGCAACCATTTAGTCTCATTGTA
GTATGAATCACTCAATAAGTTAGCATTTTTGTGATTGTTTCTTCCAAAAA
CCCTAAATCGGAGAGGCAATTCAAGAAACAATGGCTGAAGAATGTCAATC
TCGGAGACAACTGAATCCATGGCTGCTTCACCTTCAAAAGCTCGCCCTTG
AGCTCAAATGCCCTCTTTGGTACATCTCTCTCTCCCCCCTCTCCCTCTCC
CATCTCTCTCTCTCTATCTCCCCCCCTCTCCCTCTTTCTCTCTCTCTCTC
TCTCCCTCTCTCCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
TCCCTCCCCCCCTCTATCTGCTTGTATATACTGGTTTTTGGTATTGATGT
GATTTTAAATGTTAAACTTTGTGAATCTTGCAGTCTTGAGTTACTGCGCC
AGCCTGTTTTGCTACCCTGTGACCATATCTTCTGCAAGTTTGTAACTTTC
CCTGATCTTTTTTCTTCTTCCAATTGGTTTATGTTTATTCACTTGTTTGG
TTTTGTTTTTGTTTTGTGTGGTTCTAATAAGATATGTTCTTGGTTTGTTT
ATGTGTTTGCAGTTGCTGTATTAAGACTTCTACTAAGTTTGGATCTGAAT
GCCCTTCTTGTCAATCCAAATATGCGGATCAAGGTATGGAGATGTATTAA
TGTGATAGAAATTATAATAAATTGCTTTAAAGTTATGCGGATTTTTGGTT
AATTACTCAAAAGGTTTGTTCACCTTTAGATAAATTATTATGATTGACAA
CACCTGATTAACATTGTGTACTTCTTTACTTTCTGGCATAGGGGCAAGAT
TATTGTGCATTTCACCATTTTGAGACCTTAGATTTGTGTGTGATACACTT
GTTTTGTGACAACTTGTGGATATTTCTTATGTAATATAAACAAAATGGAA
CTGCTTACTTTTGTCGATGTTATATTTTTATTAGCGGACTCGATATTATT
TTAGATATTTTATTAATAAAACATCAATATATTTACTTGTTCAATAATTC
AATCAAATCTTGCAGAGATGACAATTGTAATTGATTTATTAGTATTGACA
ATAATTTCAGACTTCTGTTATGTTACTTGCGAACTGGAAGCAGTATTTGA
CTGCTTATTCATAATTTTGCGGCTGTATGATTTTTACCTATTAAGCTGAA
AGATGGACAATTAATAAATATACTTATTCACTAATGTGATCAACTTTTTC
AGAAGTGAGGTCTGCGCCTTTCATGGAAAGTCTTGTGAGCATCTATAGAA
GCTTAGATGCTACTACCGTAAACACCCTCTTTCAAGCCATTCCTTGTGGT
AAGAGGTTTGGTATTACTATAATACCATCACAATCTGTTCTAGATTTCAC
ATTTATTATGATATACTAGTTCAATATTCCTTACATTTATGCTGGACTTT
TTGTATCTATATAGGTGGTGAAAAAAAATTGAATCAGTCTCCTGTCTCGG
TTAAGATAAGCTCTGTGAATGGGACTAAGAACAAGCTTAACCAAGTGGAT
GCAGATGGAAATTCCAGCAGTGGGACATTTTTCCCTTTATTAGCTAAGAA
CTGTGGTCGTAATGTGCTTAATGATTCGGCTGAAGAGGAGAAAATGCTAA
ATATGATTGCGGTCAAAAGTGCAACTCCAGGAGGTGTTCAAGACAAACAC
ATGGAGGTGAATGGTCTTGATGGATCAGTCTTTAATGCTGATGGTAGGGT
TGCAAATATCCAGCACCCTGGTACGGATGGAAGTGTAAATCCTGAAGTGA
ACAAAGTGGAGGAAATAGACATGAATCAGATGGGACAACTTTCACCCACT
TGCACAGATTCGTTGGGTGATATGAATGATAACAGCTGTGATCCAGCGAG
CAGCAGGGATGCCAAGAGACAAAAGAAATCAAGTTCTGAACATGGAGGTG
GAGTGTGTGCATTCTGCCATTCTTCAGAGGTCACGGATGTAAGCTCTCTG
AAATATATGCTGCATTGTAATTTATTTACTCTCTGTTTTGTTTTTCTTCT
TTGTAACCATCCAACTCTAATACTGTTATATAGTTTCTTTAGCGATATGG
TTGGTGAGAACTAAAATTTGGTTTGTGGATATTCTATGTACTCATCAAAT
GTTGCTCTATGGTGTTTCTGTAGGAAACTGGGGAAATGATACATTATGCT
AACGGGAAGTTAGTTGCTGGGAGTGTGAAACCTTTCTCCAATGGGATTTA
TGTTCACAAGATATGCATTGATTGGTATGTTACCTTTGATAACTTTAATA
TTGTTGTTAATGGTTGTATAGAATCTGAAGATGTTATGCAGCTATTTCTA
GTTACCTTAATAAGTACCACTGGATGCTATTATCTTATTAGTTATAAAAT
TGTCTTATTGGTTTAACTATTCAGATTTGTTATATGTATATGGTCCAGAG
TTGTTTCATCTGTGCAGCATGGCAGTATGAGTAAATATGATTACCCTTAT
TATTATCTACAAGTCTTAGCTATATTAATCTGCATTTCAGGACGCCTCAA
GTGTATTATGAAGGTGACTATATCAGAAATTTGGAGTCAGAATTAGCGAG
GTCTTCTAAGCTAAAATGTACTGCATGTGGGCTAAAAGGAGCTGGACTTG
GCTGCTTTCAGAAGTCCTGCAGGAGAAGTTATCATGCACCTTGTGCAATA
AAGATTTCAGGTTGCAGATGGGACTTTGTAAGTCTATCAAGTTACTTTAA
CATTTGTTATACTGTCAGCTGCAATAATCACTACCATGCACACACAGAGA
TATAAATGATCCCTATTTATTTAAGCCTTTTTATTGTGTGTATAGGATGA
CTATTTAATGACGTGTCCAGTTCATAAAACTGTCAAATTTCCGGGTGAAC
GGTCCAAGTTTAGAAAGTCAGCTATTCATAAAGCTGAATCCATTGCAGCC
CCAATGTACGGTTTGAATTTGATATATGTATTTTGATTTTACTTCTTGCT
AATCTATTTGAACGTTTGATCAGCCAACTGTTTTCGTATGTAATCACAGT
GCTATTTAAAGCGCATGTGTGAGATACAATATGATTTGCACCTGAAGCGC
ATTGCTTCAGAGATGCGATGCGCTCACTTTTTGTACACATATATAAGATA
CACATGTCTTCTATTCTTGCATATAGATAGACACATATATAAAATACACA
TATCTTGTGTCTACTGATTTAGTTATACATACAATTGTCATATATACACA
TGACTTGAGGATGATGAAGAAGACTTTGTTGAGGATCGGAATCATATTTG
TGAAGATGATGATTTTGTGAATATTGATGACAAAGAAGAAGAATGGACTA
ACTTTGCAATTTTTTGTTACTTTGACTTAAAATTGTTCTACTTTGGATCT
ATTAATCTGATGATGAATTTGGTTGCTTTATCAATTAAATGTCTTCTTAT
CTATAACGTAACAGTATTCTACATTATATATCATTTATATATGTACATTT
ATTGCTTCGATGAATTCGCGCATTGCGTGTTGTGCTTATGCTCCAAGGGG
CCTTTGCATTCCATTGTTCCAATTGTCTGTTAAAGATTAGTTCAGTGAAA
ATAGTTATGGAAGGTAGACATTGCAAATGCAGTTCTCAGTTAACATCATT
CATTTTTTGCCTGATTCAAATTGCTATCCTACAAGAAGTGATTTTGCACT
CAACTACTGTTATAGAAGTTTTTCAATTTCACTCATCTATTAACAATGGA
ATTATATAGAAGAATTTATTGTCCTGCATTTCTACTCTCTAGTTTTTTAT
CTAAGATACAGTCTCTTCTTATTCTAATTGTGATACTGGCATCATTAACT
ATTTCAATCTTCAAATGGTTGCAGTTTTTATGCCATATTAAATCATGTGC
CATGAAGCTGCGGTTGATGTCTCTTTTTCTTTTATTTTGTTTTCAGAGCA
CCGAAACAAGCAAATTTTTGGGCATCCTCGGTTACTGGATTAAAAGATTG
GGTGTTATGTGGATCTGCTTTGTCTTACGAGGAGAAGGTTCGTTATTTCT
TCTCTTACAAAGTAGTCATTAAATATAAATAGCAGATGTGATTATGTTTG
AACTGAGTATCTTGCAAATTTTAGACTAGTTTCAGTTTCTTCCTTTGGAG
CATCCTACAGTTTCCAAATATGATAGGAGGTATCAAGTCTGATGACTTCT
AACAGAAACTCTTACTGATTAAATAAAATTAATAACTTCCGTGTGCCCTC
TGTCTAACCTTAATAACTATTTTCTGTTGGCATCTTTAATTTGTTAATTA
TTATGTAGCTGTCTGTTGATGGAATCAAGTAAAATTGTTTGTGTTTTTTT
TGCAGTAAGAATGTTTCTAAGGTTCTTGTAAATATAGGGAAATTGCTTAA
TATACAGTACAACTTCCATTTATAAGGATTTAAAATATGTTAATATACAC
ATATGTACACATGTACAATTAAATTTGAACTTAATCATGGATGTTATAAC
ACCAAGTAATTATTTGCAGAACAGGGATGACTTGGCTTTAGTATTTTGTG
ACATATTTTCGTCTAGACTTTGAAAGGACTCATTACTGTATATGTCAGGA
TGCTCATTACTTATTGTGGAATTAATATCATGATATATGAACTTCTCATT
TGCAGTGTTATCTAGCAAAGTTTGCGAGCACTTGCGGTGCCACTATTTCA
AGGTCTTGGAATCCAAATGTCACCCATGTGATTGCCTCAATTGATGCTAA
TGGTGCTTATACAAGGACTTTGAAAGTTCTCATGGCTATTTTGCATGGAA
GATGGGTCGTCACGATGGACTGTAAGCTAGATTCTCTGAGTTGTATTACT
CTTTTTAGTTGAAATTGAGACTTATGGATTGGCATTGACTTTTGAGTACA
TTAATCTTGTTGGATATTTGTCCGAAGTGATCATACCAAACTAGATGACA
TTTATAGTTCTCTATATACATTAAAGTTGCAAGATATGTCTGTTTTCATC
TGGACATATATACTAAAAAACCGACCATCCATTGACGGAATACAAACTAT
GCTGTGCTTGTAGGGATCAAAGCTTGCAAGGAAATGAACAAACCAGTAGA
TGAAGAAGAGTATGAGGCTGTCTTAGACACTCACGGCTGTTGGTATGGCC
CCAAATCAGGCAGGCTTCAGACCTTACAAAATGTAAGTGCATATATTTAA
TAAGCACCTTTGTTTTCTGATAGTATTAAAAGAATCATGGATATTTCCAG
CTTTCCTTTAGCAGGAAAACAGAAGCCCTAGTCCCCTGTTTTAGTAAGAA
TTTATATATGTTTCTAAGTAAAAGCCCATATATACATTTTAACTTTTTAC
TTGTCTTAAATTGGGTAGATAAATATGCTTGGTTTTGACTGTAAGAATGC
TTGGTTTTATTTTATTGAGCTCTTTGGTCAATTATTTCTCAGTGAATTTA
TTGTCTGTGACATTAATCATCTGAAACTTTTTATGCAGGCACCAAAGCTC
TTCAGTGGCATGAATTTTTACTTTAGTGGTGATTTTTTTCCAGCATACAA
GGATGACCTTCAAAATTTGGTCACAGCAGCTGGTGGTTCTGTTGTAAAGA
CTAAAGAACAACTGGCCACTCTAAGTTGTGCTGGGCAGGGATCTTCGACG
ACTCTAGTTGTATACAATGTTGATCCAGTGCAACCATACACCATGGACAA
AGGAAACTCTGTTGTGTTGCAGAGGCATAGAACGGCAGAGGAATTAGCTA
CAGAATTTGGTTGCCAGGTTCTTAAGCATATCTGGATTTTGGAATCTATT
GCAGCATGTACGTTGCACCCCTTTTTTTGAAAGATGTAAGCTCCAAGTCA
CCGGAAAGGGCTGGAGACATGCAACTTGGGAAGCCAAGAAAGACTTAGAT
ACAACAAGATTGTGTGTGTCTGTTTCAAATTTCAAATTCTTTTCTATATG
GATTAGATACAATAAGATTCTTATGAACTTTCCAGATTATGATGGGGCAA
TAATATTTTATATTGACTTTTTAA