| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017367644.1, is a part of gene, LOC108199702. |
| The genetic_marker, MK003417 K0861, is located in gene, LOC108199702. |
| 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_017367644.1 | XM_017367644.1 | mRNA | DCARv2_Chr8:21420311..21426126 |
TCCTACATAAGATGTACAGACAGATCACGCCTTCTCAGGAGCCAGACAGC
CTCTGAGATCTGGTAGTAACGCAATCACACAAATGAAGCCACTCAACAAT
GGCGATCTCTTCAAATCACAAACCTTCGTCAAATTCTTACTCTTCTTCTT
CATCTCAGTAACTTTTTTTTACCTGGGAAAGCATTATTCCGACAACAACA
ACAATCAAGCTCTCATTTTTTACAGTTCTAAACAGTCCCCTCTATCTTTC
TCCGTCACTCTCTCTCCTAACTTGAACAAGCAATTCAACATCTCGTCTAT
AATAAACGACACCGTTTCTGGGTCTGAGCCAGAAACAGCTCCGGGTGGTT
CAGTCACCGATGCGAAAAATTCGCCACCGCCGGAGACTGCTCCGGCGCCG
CCGGTGGTGCAGAGGATGGGGGTGATTGATGAGAATGGGGTGATGAATGA
TACTTTTGAGGTGGGTGAGTTCGATTCGAGTGCGGTGGAGGAGTGGGAGA
GTGAGAATAGGACTGAGAGTGTGGAGGGGGAGAGTGGTGGAAAGATTAGT
GTGAAGAAATTTGGGGTGTGTGATATGAGTATGCGCGATTATATTCCGTG
TTTGGATAATGTGGAGGTGATCAGGAGTTTAGAGAGTAGTGAGAAAGGGG
AAAAGTTTGAGAGGCATTGTCCCGAGAAGGGGAAAGAATTGAATTGTTTG
GTTCCGTCACCTAAAGGTTACCGGACTCCTATTCCGTGGCCTAGAAGTCG
GGATGAGGTGCGAATTCAAGCTATTATTATAATTATCGATGTTTAGGTTC
TAATGATTTGTTAGTAGGTGTTCTAAATGATAGAAATATAGGTGTTGGTA
GGGGTGGAATTAAGATATTATGCTTTTGTTATGTTTTTAAATTGTGATTA
TACTTGAATTGTGGAAATAGCCATTGTTAGATATTTGAATTTTAATCTGA
TATAAAATTTTTGAAGAGATTATTTATGAGTATAAATGCAATTCAGGTAT
GGTTTAGCAATGTTCCACATGCACGTTTGGCTGAAGATAAAGGTGGTCAG
AATTGGATTACAGTGGACAAAGACAAGTTTAAGTTTCCAGGAGGTGGAAC
ACAGTTCATACATGGGGCTGATAAGTACTTGGATCAGATTTCAGAGGTTG
TTTAGCTTTTTGTTGGATTTTATATTTGTTGAAGCTGAATTGTTTATATG
TGCTTACTTATTTTTTCCATTTGAATGCGTAGATGCTCCCTGATATTGCA
TTTGGCCGTAATACACGGGTTGCTTTGGATGTTGGATGTGGTGTTGCGAG
TTTTGGTGCTTATTTGATGTCACGGAATGTGCTTACTATGTCTGTAGCTC
CAAAAGATGTTCATGAGAATCAGATTCAATTTGCGCTTGAGCGTGGCGTA
CCTGCAATGGTGGCAGCTTTTGCAACACACCGATTGTTATATCCAAGTCA
GGCTTTTGAGCTAATACATTGCTCGAGATGTAGAATTAATTGGACTCGTG
ATGGTATGAATTTTTTTCCAGCATATGTATATAATTGCTAGGAAGCATTA
TTGGCTATATACTAGTGGTTACTGACAGTATTGTTCTAGTTACATGTAAG
TAGAGACACCACCAAACTGGCTGAACTCCTAAAATTTTAGCAATGACAAT
GAAGAAATGCTCTGACTAATTGCATTAGAGCTCCAATCTTGGAAAGCGGA
GTATTAATACCAAAGAAGCTTATGCCATATACTTTTCTGTCTATTACTTA
TTATATTAGTTACATTGCCGCCTTATACATTACAAGATGCCAATCTTACT
GGAAAACCCTTCATTGTGTTATAGATCAGTTTACTTAAATTAGTCAGGGG
AGAAGGATAAACAAGTTGTCTTGCACGCTGATATTGATTTTTTTACTCGC
ATCTGAGCATACTGTAACTGCTACTTTTTTTGTTCATTTAATAAGATGGC
ATCTTGCTTCTGGAGATCAACAGAATGCTACGTGGAGGAGGATACTTTGC
TTGGGCAGCGCAGCCTGTTTATAAGCATGAACCACTCTTAGAACAACAGT
GGGAAGGTGAATAAACTGAATGTCTATTGGTGATGTTTATAGTTTTGATA
TCTTATAGGGTTTTAGATATTTTTTTATAGATGTATTGTTATTTCTTCGT
GTCTGACTAGAAAATGACTACTTAGATGCACTTGATGTTTGGATTAATGA
CACGGAGATACTTCCTGAAGTCTAGTTTGTGTACCCTATACTTAAGTTCA
ATCTAATCCACATTCATTTGTAGTTCTTGTGCACCTATCAACAGTGCCCA
TTCCCTGTTAAGCTGAAACACATTTTTTTATCACTTCCTATTAGTTTCAT
GATGAAGGCTCACTATAGGATAACAATAAATTAAACATTGATGGTCACTA
GAACTGTTGCAAAACTTTTCTCCCAGGTGACTGCAAACTTGTTTTGTTGA
ATGAATTTGGATGCTTTAATTGTTCTGTTTGTATCCTGTTTTACCTCGAA
CACAATCTTTTGATCCGTGCTCATCCCCAAGTGGTTTCATTTTAATTCAA
AGAATAGTAGTAATCCTGATGACGGGTGAGGAAGGGGTGTTTTACTAACA
TCTATGAGATGTCTTGTAGCCCAGCTTCCTGGTCCAGTTGGGCACATCTT
TCATGACATTATTACAATTTTTATTGGTAACATATGATGAATAGGAAGGA
ACACAAAAGAGAAACGAAATGTACTTTGGTTTATCATATGTTTGCCATGT
ATTCTTCTATAATTGGTTTGAACAGATTTGCAGTTATTTTTGTTTAATGC
AGGGTTTATTCATTTTTGCAATATTTCAATCTACAAGTCTGGCTCTTTCA
TTCACATATATTTTCATTGACTTTTGTCCGTTTTCAGAAATGGTTAACCT
TACCACCCGCCTTTGCTGGAATCTTGTAAAGAAGGAGGGATATATTGCAA
TATGGCAAAAGCCTATGAACAATAGTTGCTATTTGGAGCGGGAGCCAGGG
ACCCAACCACCATTGTGTGAAACTAATGACGACCCGGACAATGTTTGGTA
AGCTTTCTATGTACTTGCATGTTGTTCAATGGAACAAAACAATGCCCCTT
CGTCTTAAACAACTAAACGACACACTAGCTATCATAGTAATAATGCTTAA
ATGTAGCTTTTAACAAGGAGTCTGCAAAATCTTCATTTGTGAAAAATATG
ATGTTTCCTATATCATTTTTCTATTTTGTTCTATGTGATGCCAAATATAT
GGATAAGACTTCCTGTCTTATTTGGTTTGGTAAAGGGTCAGCAGTTCCAG
TAGACACAGGTGGAATCTGGCTTGGTGCCTTATTCGGCTAAAAGGTCCAC
ACTTCCAAGTCTACCCAAATTTCTATCACAGCTTTTTCCTTTTTTCTTTC
TAAATACTGAGTATGGCCTATTATTTTTGTCAAAATTTGTGTTGGTATCC
TGTGTGCTTGTGCTTGCGGTATATGCGACTTGTGCATTTGTGACCAGAGT
CCTCAACCTCATTTAAGGGGTTTAAGAAATTTTACTTTTACTTCTACATT
TTTCCCATTAATTGGTGAGTTTTTTTTTTTGAAATCTGATTTCGCTGTAT
TTTTCTTCGTCTCATAACGATCAATTTGCATACCATGTGTGCTATAACTC
TTCGTGATTGAGATTTTTTTTTTATTTTTAGTTAGTAGTTTGTATATAAA
GAGGTTTGTATCAGAGATGTACTATTACTTTTTTGTTGAGTAAAAATATT
ATCCGCGAGAGGGATGTTTATGTTGGTTTAAGTCGATTTGAAATGAGATA
ACCTGTAAATGGAGAGAGCATCATGTACTGTTCTTTGTATGTTTGCTTTT
AGGTATGTGAACTTGAAGGCATGCATCACACGGCTACCTGAGACTGGATA
TGGAGTTAATGTCACAACTTGGCCTGCACGATTGCAGAATCCTCCTGACA
GGCTTCAAAGCATACAACTCGATGCTTATATATCACGAAAAGAACTCTTT
AAGGCAGAAGCAAAATATTGGAATGAAATAATAGAAAGCTACGTACGTGC
TTTGCACTGGAAGAGTTTCAAGCTTAGGAATGTGCTGGACATGAAAGCTG
GTTTTGGAGGGTATGATACTCGTATTCATTTGCTCTAATTTATAAGTCCT
AAATACAAACAACACCATTTAGGACATAAGCTAAAGCTGATTCCTTAATC
ATAAGTGCACTGCTTTTGCAGTTCTCTAAAGTCTGTTGTTTACTTATAAT
CATTTGGTTTGCTTTTCAGATTTGCAGCAGCATTAATAGAAAACAAATTG
GATTGTTGGGTTATGAATGTTGTTCCTGTAAGTGGGTCTAATACCTTGCC
TGTTATTTATGATCGTGGACTTCTGGGGGTTATGCATGACTGGTGAGCAT
TATTATGTCACTCTCAATTTTGTTGTCTTAATACGTTATATATGCAGTGT
CATGAATATTTCATTACAAAAATGTTGGTCACCCAGTTTAGAAGTCATGT
TCAATAGTTCAAGCACGAAATCAGGTGCACTTTTTTGTTCGGGATGAGGG
TAAAAATAAATGCAGTGCAGTCGTTCGTTACTGCTTGCTGGAAAAATGCA
TTTTGTCCTACAGTTATGAATTGGTTTCTACTATTGGGAAATAATAGGAC
AAGTAACATCTTAAGCAATAGGTAATTGGATCTGATTTTCAATGGGCTCT
GGCCTTGGTTTGGGGTTGTGACCATCTGAGTGCCTGGAATTTGCGTCTGT
CTCTGTCAAAGTCCTTGCACAACAATTGTGCGCTCCGTTATTGTCGCAAA
TAATGAAAGACATACACTATTATATATTTTCTGCTCTAATTAATTAAAGC
TAATCATGTTTACAACACTTGCCAGGTGTGAACCTTTTGATACATACCCG
AGAACCTATGATCTCTTGCATGCAAATGGACTTTTCTCTGTTGAGAAAAA
GAGGTAATTCTACCTCCTTAATTTTGAGTATATATCTGAATCTGATGGAT
GGTGATCACAAACCCACCCCCTAAGCATGTTACTAACTAATGATGAGTCA
ACAAAAATCTAAAGAATACAAAATTGTTTGGACTTGATAATATGAACACA
TGTTGTCCTTGTGATATAGAAATTTAAGTCCAATATATATCACTTGTATG
TTTTTGATGCATTTTCTTCTAAATTAGTTTGTTCGACTTTCTTTTACCAG
ATGCAATGTCTCTACCATTATGCTAGAGATGGATCGAATTCTGAGACCTG
GTGGACATGTATATATCCGTGATACCCTTTCAGTAATGGATGAACTTCAA
GCTGTGGGAAATGCCATTGGTTGGCATGTAAGTATGCGTGAAACATCCGA
GGGTCCTCATGCAAGTTATAAGATCTTAACTTGTGATAAACGTCGGAAGT
AAATCAATTGAATTAGGTATTGTAGTTCGATTTGTTTTAAGATGGACAAA
GCATGGTGGAGCTTGTTTTGACAGCGCACTACTTTGAGGTTTATGGAGAT
AACGACGTTCAAGTGGAGTCCAATGTTCTGCAGCAAGGGAGGACAGTATG
AAAGTTGTACAAGCATTTGAGAGATTCCCCAGCGTTCAGCATGTATCAAG
CAAATGTATAGCATCATCCAGTGTTAAAAGAAAAACGGACGCACCAGTAT
AGTAAAAGAAATGCAGATAAGATATTTCCATTTACTTTTCTTGTAATATT
TAATTAATTTAATTTCTTAATATAGTAAAGATTAAACTGATATCTGAAGT
CTTCACTGGGTTTATAACATTACATTCTGTTTCTCAAATCCAGGGAGATC
AAATGGCTTTCTATA