| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017387768.1, is a part of gene, LOC108215319. |
| The genetic_marker, MK005075 K2519, is located in gene, LOC108215319. |
| The mRNA, XM_017387767.1, is a part of gene, LOC108215319. |
| 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_017387768.1 | XM_017387768.1 | mRNA | DCARv2_Chr3:8016556..8022632 |
| XM_017387767.1 | XM_017387767.1 | mRNA | DCARv2_Chr3:8016557..8022632 |
TACAACTAGTAATCCAGTATTGTAAGAAAGCGAAGACAAAAAACAGTTGG
GTCAGCGTTGAAGACTTTTGCTAAAATTCACGAGATTCGGGATCATAATG
ATGCCCTCTATTAACGCGTTACGCATTACTATTACACAAACACACAGTGT
CCGATTCTTGGATCTACTCATCATCAACCAAACCAAACATCCTATGTATT
GGACTCCGAGCTGTTAGTTGAGACAAGTACATAAAACATGGGAGGGTTAT
GCACAGGGGGTACTATCAAACATCATCGTCAAAGTCAAGGCAAAGCTGAT
CATGATTATTCTTCGGACAACAATTCGAAGAATATTGATAAGAAGACCAG
CGATGGGCTGGAGGAAGAGGAGAGTTATGATGGTGGAATGAATGGGTCAG
CTGGTTTTGAATTTTATGAGAAGAAGAGGACTCCTCATATTTTCGATTCC
GGCGAGCTTAATTTTAATATTTCTAATCAGTTCTTGAATCGCCGATCAGC
TGCTGCTCGGACTCCACCTGCCACTAAGGTACGCTACTCTCGGTTGTTTA
GGCTTCTATGAAGTATAGTTTTTTTGGAATATAATTTCTTAACATTTTAA
AAAAAAATTATTATGACATTAAGCCTCAGAATACGTACCATAAAATAACA
TAAAGAACTTGTTGGGATGGGACAGAGGGAGAGGGAGTATATTTGAAGAC
GCACGGGTCGCGTTTCAGTGCAAACTATGTTAAACCAGCAGAATTTATAT
GTATGATTCAATGGATAAATAAGGACATCATTTAATTTGAGTATACAAAA
GTACTCTAGTTTAAAATCAAAAATATAAGATTCACTATAATACCAAGAGA
TTTCATTAAATATATGTATGAAATAAAATGTATAAAAAGTAGTACATGTA
GTTTGTAAATAAAATTGTTTGTGCTAGAACGCTAGCCTTATTCTTGTTTC
TTTGCTCCCTGTGGCAGAAAATAAGATTGTTCCCGTGATCATAACACTGC
ATTTTCTTTCTTTTTTAGTTCAAGCTCTAATTCGTTTGTACACGGAATTG
GTGCATCAATGTAAGGGGTAATTTTTTGGCTATATGGTAACTTAATTATG
GTACCAACTCGCAGTTTCTAGGTCTGAACTAAAAAATGCTTATACATATA
CAAGTGAACAAGAGAATAAACTTCAACTGTAGTATCTGCGAAAAACTTGA
AGGAAAACTGTCGAGGCATAGGGAAGTGTAAACTTTAACTTGACGAGTAA
CATGCCACGGAGAGGTGATAAATTCCTCGATCGAATGACTGATAGGTAAC
TGAAATTGGCAGCAACTTGCAGTTTCATCACTTAATGGAAAAAGTTTCTG
TCAACAAATCTTACCAACCTGGCCTGAATTGCCTGGTTTTCTTATGAGTC
CATCTGCATTTCTATCTATAATGGTTAACTGGTGCATATCTCTTTAAAGG
TTGAAATTTGGTTTTATTCAGTGGTACATTTGCAGTTTCACATGATTTTA
AAATATATGCATATTTCATAGGTTGAAGTTGTGGCAATTGAATTGTAAGC
TAGGTGGAAGTACATTCTAATTGACCATTATATGTGAAAAAATACTTTTA
TATTAACATTTAATTCCAGTTCACATATGTTGTTGCAAGAGTTCATAAAA
GGTTTTTCCCAATTTACTGAACTGATTCCTAGTTAGTCCAAAGTCCAGTA
ACCAAAGAACCATTTGACCTGATTCGTGTTAGTGACGTTGAAAGTGTTGA
CATTGTTTATTGCTTATAGGATGAATTCTATGATTTTATAGATATATAGC
AGGTGTATTTTGTTAAATAGTTGTGATAATTTCAGAAATAATTTGAAATC
TAGTTGTATATTATGTAATACATGATGAATAGATTGTTATTACAGAATAC
ATGAATTAATATATAATTATGCATGTTTGGTATACAAAAATTAGGTAATG
CAGAATTAGAGGAGATGTATAAATGTAATTAAACAGGTTTCAATATAATT
AATATTTTGTAAACACGTTTGGTCAGAAACAACCATACCTGATATATATG
TGAACAGGTATACGTTCGCACATTACATTTAAAAGGGCAACTACGGCAAC
ATTTTGGTCTTTGTTAGTTTACTATGGATATATTATGCTAGTCTGCTCTC
TGCTGCCATACTAAATATTGAAAGAAATTTTTCTTGCATTTTAGGGGCCT
CATATGAACTCATTTTTTGGTAAAGCTGGCATTGCTGGCCTAGAAAGGGC
AGTAGATGTCCTGGACACGTTAGGAAGTAGCATGACAAACATGCACGCCG
GAAGTGGATTTGCATATAATCTGGCTTCAAGGGGAAACAAAGTATCTATT
CTTGCATTTGAAGTTGCTAATACCATTGCCAAAGGTTCCAATTTGTTACA
ATCTATATCTGAAGAAAATATTCAAATACTTAAAGATGAGATTCTGCAAT
CAGATGGGGTACTGCGATTAGTTTCTACAGATATGACAGAGCTGCTTAAA
ATTGCGGCTATCGACCAAAGGTTGGCCATAACTGGAAAACTTATTCTAAT
AGGCTTGTTTCTTCCTTCATTTCACTTACCAAAATAATTTCATTCAGAGA
ATTTATCATACTAATTGTTTATATGTAGGGAGGAATTAAATATATTTTCT
CGAGAAGTAATCAGGTTTGGAGACCTCTGCAGGGATCCACAATGGCACAA
TCTGGATCGTTACTTTTTAAAGTAAGTTTTGTTCAAGGAATATGACAAAA
AAAAAAAAAAAAAATTGTTCAAGGAAATGTATTCAAATGATATATAATTC
TTCAATTGAAATGTAATGTGATGATTATAATTGGATGTAACATGTCAGGT
TTGATTCAGACCCTGCAGCTGGAAAACTGCTTAGAGAACAGGCAGAGATG
ACAATGCAAGAACTCCTTAGTCTGGCTCAGTACACATCTGTAAGTTGTAA
TATCCCCTTCTATCTTGTTCCTAATTATAAGCATTCAAAGGGATATATTC
TTCATCTTACAGAGAGACTGTGTATCCTTTTCTGATAAAACAATATTCCC
TCAAACAACATTGTGCATTGGTAACTGATCTTGAAGAATTTGTCCACCAC
GAAGTCTGGAAATCTTATATTATTATGTGATTAACATTACAATACATAGT
GCTAGGATTTGGTGGTTCTGGACTTCTACATGATTTTGGAGATATCTTAG
ATGGGGTTAGAGTTTGCAATTTATACACTGCTTTGTGTGGCTAGTTTGTA
AAGTAATTGTTAGACAGTTTGTATTTTTACTCATTGTAGTATATTTTGTG
TTTTTGTTGGAGATAGTTTTGCTTTGCTTAGTGAACAATACTTACACACC
CATATTTGCATACTCCAAATGAACCTTTTACTTCATCTAAAGGGAGTGAG
GGCTATAACACAAGAGCAAGAGCGCTTTGGCACCTATAAATTGTTTTTTC
CTGTTGTTTACTGTTTTCCTTGGTGGGTGGGTGGGGGGTTGTCCTAAGGT
GGACTGGCTGAGACCACCTATAGTTACTGTGTCTTGTAAATGTGTATTTT
GCAGGAATTATATCATGAAATGCATGCTTTGGATAGGTTTGAGCAAGATT
ACCAAACGAAGGTTGAAGAAGTGGAGTCTTTACATCTTCCTCGTAAAGGT
TTGACATTGTGGATCTCTTTTTTTTTTCCTTATTCTGTGCTAAAATAATT
GAACACGGATTTAGTTCAGAATAACAATTCAATCCAGGTCCAAGTTCTTT
TTACTTTTACTACTATATCTGCATTATGTATCATTGTGTGCTCGCAGCAG
TAAATCGTTTCTGTTCTGTACAGGAGAGGGTCTCTTACTATTACATTCTG
AGCTAAAGCATCAGAGGAAACTTGTAAAGAGTTTGAAAAAGAAATCACTT
TGGTCTAAAAGTTTGGTGGAGGTAATGTTCTGGTATAGGAATACTTGAGA
CTTTGAGCCCAAACAAGTGAACTTTTGTTGAACAATAATTCAATTGTTCT
TTTGTACTCCAACAATGTGGATTTGATTCATACTAGTTTTGGTAGTTTTA
TGTCAGTGGGGCACACAAATTGACTTCCATTCCTCACATGTTTGGTTAAA
AACATCAAGATCTTGAACCAATTTTTCACTTCCATCTGAAAGAAAGTCGC
ATCTCTTACTATATATATTTTGTATTCAACCTTTTTATACTACCACTTTT
TTTAATACAGGTAGTGGAGAAGCTTGTTGATGTAGTCACCTACATACATC
AACACATCTCGGAAGTGTTTGGAAATGATGGTACGAGTACTATGCTTGAT
ATACAGATAGTTTTGAATTTTCAGCAGTATTTGTATGTCTATACTGTGAA
CTTTGATTTACATCAGTTATTGAACGCAGAAACTTTTCATTCATGAATCA
TGTAGCTTTGTGGTATATCAGATATCTTATCAATAGCTCATACCTTCACT
TTCTGCTGTAATTAGTTTCAGGTGCATCATCTACCGAAGAGAAGTCCTCC
GGCAAGCCTGATGAAAGACTGGGCATTGCTGGTCTTGCTTTACATTATGC
TCATATAGTCACTCAAATTGATAACATCGTAAGCGCTAGTCATTCTTCTG
TCTAATTGAACTGCTGTTATTTGAATGAAACTCATTGTTGGACTAGGCAT
CTTCACAATCCTGCCTCTCTTCCTCCTAATATTAGAATGGACTATACTGT
AGGGTGTTTTAATGTCGGTGTATAAATATTTAACTGCTGTTAGTTAACCG
AAGATCATTATTGTACTAGGCATCTCGTCCAACCTCTCTCCCTCCTAATA
TGAGAGATGGACTGTATAGTGGGTTACCAGTTAATGTGAAGAAAAGACTG
CGGTCGCGTTTGCAGTCATTGGATGTTCATGAAGAAGTATGTTTCCTTGG
CAAATTTCATTTGTATCAGTAGTTTATTCAAGGACACACTGTATCACTGT
CTCATTTTTCATACTGTCCTCGTTTCACAGTTGTCCATTCCTCAAATGAA
AACTCAAATTGAAAGGACACTCAAATGGCTTGCTCCTATCGCTGCCGATA
CGACCAAGTATGTAACTCATTTTCCCGTCTGCTCATCTGCTGTGGTTCCT
CCTCTGACTTCTGAGTCAATTGATCACAATAGTATCAATGAGCACAAATA
GTCTTTAATTATTATTCTAAGCTAAAAACAAATTCTTTTGTGTGAATGTG
AATTGGCACAGAGCGCATCAAGGTTTTGGATGGGTTGGAGAGTGGGCAAA
TACTGGGTCAGTGGACATATGCTTCTCATGTCTTTCCAGTGTATAAATTA
TTTGATACTCTATGGCCATCATGAGGACTAACAGTGTTTTCCATTTTTGA
CAGTATCGAATATGGCAAGACAACAAAGAATAGTGTGATTCGACTCCAGA
CGCTTTATCATGCTGATAAAGGGAAAATGGATCTCTACATTCTTGAACTC
ATTATCTGCCTTCATCGCCTGATCAGCCTCGTAAAACACAAAGACAACGG
ATCCAAAGCTCAGCCACTTCAATCTCCAGTTGAGAGAGAATTGGTTCCAG
ATCACGAGATACCGAGTGAAGTACAGAACACTATTACTCTAGAGGATGGA
AATGTAATAGATAACTCGATGAACCGGCAAAAACTGTTTGGCAAGAGCAA
AAGCCTAGAATTTGTAATGGGAAGGAGGAAATCACTCAAAATCCGGGCAC
CAAGTAGGAGTGCTGGGAGCTCCCCCAGGACCGCAACAGCTCTGGAGCGA
AGGCAATCAAAGGCCAGCATTTTGGATGTATTGGACGGAATAGAACAGCA
TAGTGAGCTTTCATGAATCTAGTAGGAATCATTTGCCACTTTCCAGGATT
ATTTTGTTTACTAAGCAAGATGTTTTGATCAGTAGAACAGCTTTTATGAT
TTGAATCAGTGGAGCACAACCTCAGTAACATGTACATATGTATAGTTTGG
TTTTCCTCCTCCCTCTCTCCCTGTCTAATTCATATCTATAGACTTTTATC
ACTTTAAAGGATGTTTTGCTCAATTTTATGCATTCCAACTATTAGGTTGA
GGAAAGGAGTAAATGTTAATTTTGTA