| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017364041.1, is a part of gene, LOC108196651. |
| The genetic_marker, MK004749 K2193, is located in gene, LOC108196651. |
| The mRNA, XM_017364038.1, is a part of gene, LOC108196651. |
| The mRNA, XM_017364039.1, is a part of gene, LOC108196651. |
| The mRNA, XM_017364037.1, is a part of gene, LOC108196651. |
| 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_017364041.1 | XM_017364041.1 | mRNA | DCARv2_Chr7:34750271..34756351 |
| XM_017364038.1 | XM_017364038.1 | mRNA | DCARv2_Chr7:34750271..34756351 |
| XM_017364039.1 | XM_017364039.1 | mRNA | DCARv2_Chr7:34750471..34756351 |
| XM_017364037.1 | XM_017364037.1 | mRNA | DCARv2_Chr7:34750471..34756351 |
TGGGTGAGACACAGGGTGAGGTCTCTAGGTCTCAATTGTCACCTAATAAA
GCCAAAGCATGACTCTTTCTGTGACTCTTTGTCTCCACACTTCAACTTCT
CTTCATGGCACTTCATCTCTAGCTAAGGTAAATACCCTTTTTTATAAACT
TTATTTTATGCACATTTAACCTCTAGTTTACATATGGTGGAGAAATAAAA
TGGAGGGTTAAGTGGGACCCACTTGTAAAAAAAGAAGAAACTACTTGTAA
AAATTGACACCCATGATGCCTCATTTTTCAACCTTTAAGGAAGGTATAGA
TGAGCCTGATGATCTCAACTGTTTCAACTTTTTCCCCATTTTTTTTTTAA
ATTTTAATAATAATTGTTATTATACTTTCTTGGCCTGTATGCTAAGCATG
GTTTGGTTTTCAAGTGCTTTTCTTGTGTTTTTTCTTACTTTCACTGGAAT
GTTCGTCTGAAGCTTAAAGATTGAATCTTTATTTATTTTGGTAATTAAAG
AGTGAAACTTTTTTAGTTTTTTTAATTTTGTGGTATATATTTTAGTTATT
GCAGTAAATTATATTTGCAGGAGTGGTTGAAGCAAAAGGGTATGAAGGGA
AATCAAGAATCTTGTTTGTGAGTATGATTACAAGTGAATTGGGGATTCCA
TTTGATCTGGGATTCATTAGATTCAATCTTGTCAATAGATTCTTGCATTT
TTTGAGGTAAACTGTTTTGCTTGTGATGATTGTGGCAACTGTTTTACTTT
GAGAATGACCCATCAATTTCAAGATTCTTGCTTTTATGTATTTTTCAATC
GGAATTCTGATATGTGAATATATTCTCATGATTTGATATCTTACAACTGC
TGAAGTTTCTTAATTTGATGTTCTCTGTTGTGGAAGTTTTGTGTTGTATG
TTAAGGAATTTTCGATTGTGTTAGATGTTCATTCTACTGTATTAATTTTG
CAATTCAAGTCCTTGTGCAACTGTTTCAGATAGGGTATATGCGAACTTAA
TTGCGTCTTTTTTCTAATTACTGTTCTTCTTCTGCCCTGTGTCGAATTTG
GCTCAACCCTTCATATTTACATTTTTATTCTTCATTTTCGCCTCTTTTTA
TTTATATATTTGTGCTAACTTTTCACTTTTTGCCTATGCTTTCGATCAGG
ACTGACAATTCATTATGCTAGTGAAAGGTGTTCTTTATTAATTTCCATCT
TTCTTTCAAAAACCATCAATTCATTGTCATCATTTGATGCTGTTAGGCTC
TTGATGTTTGTTCAACTTTTTAGCTGGTTATTGGTTGGTGTTGCAGCTGA
CTGAAGAACTGTTTGTCTTTACATTTTTACTCTTTAGCTCAATCAAAAAT
TTTGGGATTTGAAGATGCCAATGACTACTAGTCTATATAAATTAAGAACA
TTTCTCTTTCTGTTGCGCTAGATACTATATTGATCTGCAATAGGATGAAC
TGTCATTAGCCAAATTTTATGGATGCAGAAAAAGATTTGTCAATCTAGGT
GTGGGAATAGCGACATGGGATGGTTAACCAAAATTCTGAAAGGATCTAGC
CATAGAATCTCTGAAGGGCAATATCATGGGAAATATCATGAGGAGAAATT
TTGGGAAGGCCCTTCTAATTCAGTGGTAATTAGTGATTCTGCTACTTAGA
TGTTACATTTAATAAGTAGCTTATTTTTTAGATAGATATGCTGATCCTTC
ACTGGCTTAGCAAACAAATATGCTTGAAAGATGTCTACCAATTTTTGCTT
CTTATGTGTACATGTATACTCACAATTTTTTCTTCTGTTGGTATTCTGGG
AATTGATGTAGGATGCATGGTCAGATTTTGAGCAGGAAGATATTGATCAT
GCTATTGCACTTTCTCTTGCAGAAGAAGATCTGAAAGGAAAGAAAGTAGT
AGGTAAGTTGCATGAATTACGTAGTTGTTATTCATGTAGAAATAATATAA
TTCTTAACATATGCATTCTATTTGCATGTTTCGTACTTCTTAGTAATATA
TAAGAAGTAAGAAACAACTAGAAGCTTAACATGGTCATGGCAATGTTCTC
TTACTAGTAATTAACGTGAAGGATAGCTAAGAATATTTGTGCTCTTTCTG
TGATTGTGTAACTTGTTAGTTACAGACTTGCAGTGGCTGGAAATTATACA
CGAATGCCTGTGGCACCTAGCTTGTTGCTTTTATCCTATCAATCTAAGTT
GTATGTGAGGCTTTGTGGCAAAATATAGGAATCTCATTCAATCAAACTCT
TTTATGGTGTAACTTGATATGAGTATCAAATAGAAGACTGTTACAGGGTA
TTCCTAAGCATTATATCTATCACACAATCGTTCCCAAGTTAAAGTTACTT
CGATCCCCTAAATAGGTATGGGGTCTTTCATTTGTATTCACATGTTATTG
TTTTAAGGATTGTAAATCTGATCATGCTTCCTCACTTGATATTACTTTTT
TCTAAGTTAAAAAGATTATCATACAAATGTTTGACAGTTTTTCTCAGCTG
TTGATAAACCTAAAAAACTCTATTGATTTGGTTCAAATAATAACATCACT
TTTTATTGGATTCCTTAGAGGTTAAAATAGAATCAGAACCAGAATCAGAA
TCCGAACCAGAACCTGAACCAGAACCAGAACCAGAACCGGAACCGGAACC
GGAACCAGAACCTGAAGAAGAGCCTGAACCGCATTCTGAACTGGAAAAGG
TAGAAAAACCGAAAATGGATGTTCTTCTGGAAGAAGATGAACAGCTTGCC
AAGGCTATTCAAGAAAGTTTATACATAGACTCTACACCTCAATATGATTT
TGGAAATTTGTTTCAACCATATCCTTATCTATATCCACCTGGGTTCAGGT
ATGTTCTAAATGTTTCCGTTGGCTGGTTTACACTTTTATATCATTTTTAC
CCCCTCTTTCCTCACACACACACACACACACACACACACACACACACACA
CACATATATATATTTATGTGTGTGTGTGTGCGCACACACACAGACACGTA
TATTGTTCTACAGTGTCGACCTCATTCCCTTTACAAAGATCGAGGGTCCA
TGCCTTGTCGAAGGCTATATTGGTGCTTGAGTGTCTAGTTGGCAAAAAAA
AAAAGACAAACCTATGAATCTGTGCAATAAGATTTGTATCTAGAATCCAG
ATTATTATACTGCTCAGCTGCTTATCGATCTCTATTAATAATTTGGTATT
AAGAATACAAAGGAATGTTCATATGTTATGCTGCATCAGCTGCTTAACTG
TTATGTGATAATATATTTGGCCTTCTAAGGTGTATAATTTCTGTCTAATG
TTACAGCCACCTGCACAATATGAGTTGGTAATGACTTGAAGTGTGCAGGC
CAATATAGCTCAGTTTGTAAACTTATTTAAACTACAATTGATTCCTGTTG
TCATAGCAGTTTTTGTAAAACTTTGAAAAGATGTCTCAGTTTAAACCCCA
ATATAAAGCTGGAGTATGAAGCCCGATTTATATGAAATTTTTATTGGAGT
GAAATCTTGTATGCACAAATTGCCTTCTTGATGCACAATTGCAACTTGTT
ATATTCATCTATTTCCTTATTTTCATATTAACATATGAAATTTCACCATT
TAATTTTATATGTATTCTATTGTAGGATCTGTGCAGGTTGCAACAGTGAA
ATTGGCCATGGACGATTTTTAAGTTGCATGGGCGGTGTTTGGCATCCAGA
ATGTTTTCGCTGTCATAGTTGTAATATACCAATATCTGATTATGAGGTAC
GACACTTTTAAGAATTAAAGTGGTTATCCGGAATCTTTTAAGGAAAAATT
TCACGAGGTTTTTAGTTTCTCTTCATAAACCTGATATAATTAGGGGATAC
ATATCTGGCCCTATAGTTAGAAAATGATTTTTCTTTCTATTGCTGCAGTT
TTCAATGTCTGAAAATCGGCCATTTCACAAATCTTGCTACAAGGAACGCC
ATCACCCCAAATGTGATGTTTGTAAGAACTTCGTAAGTGGCTATATTCTT
TGCTCTAGTTGTACATTTCTATTGTAAAATGAACTATGTATATTACGTTA
TGCCACAAACCGCGGGTGCTAATTTTGTGATAGATTATCAAATTACTTCT
CGCTGATTACATGTGGATTGCAGTGTTATTAACTCTGCTGTTTTAGTATT
AATTAAGTCCTATTTTAATGTCATGTTATAGATCCCAACAAATGCGGCTG
GTCTTATTGAGTATAGGGCTCATCCTTTCTGGGAACAGAAGTACTGTCCC
TCACATGAGCATGACATGACGCCAAGATGTTGCAGTTGTGAGAGAATGGA
GGTATGGGAAATTGGTTACCCCCAAAAAATCATCCCTTCCTGAAACCAAG
ATATAACTGTAAGAAGGTTTCTAAACCTTGCTTACACCGTTACACATATA
TAGCAGAAAAAAAAAGAATCTTGCTTACATTGATTAATAAATGAATTGCT
CGAAGAATTGTGAATTTCTAATAGTAATTGTAAGAAGGTACTTAAGCTTT
CTTGCTAGTGCATGAGAAATCACACTAATATAATAAAAAACAGAGCATAA
GAGAAGGCGAGGTGAGGATCAAACTTTTTCACCGACACTTGGGCATTCCT
TGATTCTTATTATAAAATACTTTCAATCCGATGCAGCCCAGGGATACAAG
ATATCTTTTACTAGATGATGGTCGAAAGCTTTGTCTGGAGTGCTTGGACT
CATCTATAATGGACACACATGAATGTCAACCTCTTTACCTTGAAATACAA
GACTTTTATGAAGGATTGTTAATGAAAGTGGAACAACAAATACCACTGCT
CTTAGTTGAGAGGCAAGCGCTAAATGAGGCCATGGAAGGAGAAAAACATG
TGAGGCGAATTTATTTATGTCCTCCATGTTTCAAATGATGGTTAAATTAT
TACTGCCTGTACTCTTGATATTCAAATTTTCTCCTATTTCAGGGTCATCA
TCACATGCCTGAGACGAGAGGTCTTTGCCTGTCAGAAGAACAAACCATTA
GCACTGTATGAATATTTTTCTTAGCATCTACTATACTTGGTGTTTTAGCT
GTTTAAATATATATATTTAATTACTCACCGACCACAGATTTCAAGGAGAC
CTAAGATTGGAGCAGGCTACCGGATCATAGACATGATTACAGAACCTTAC
AGACTAATTCGCGAGTGTGAGGTGACAGCTATTCTTATTTTGTATAGTCT
TCCAAGGTAATATTATATAAAGTTTCCTTCTATTGTCTATATTGGACTTT
ATTCATTCATGCACTTCCTGAAATACAGACTAAAACCAAACTCAAAATTT
TCAGGTTACTGACCGGATCAATCTTGGCACATGAGATGATGCATGCATGG
CTGCGGCTAAAAGGTGCTTATCTTTGCAAATCAAAATATACCCTTTTTTT
AATCATACAGCCTCAAGAATAATGATAATAATCGGGTAATTATTAGGTTA
TCCCAATCTAAGTCCAGAAGTTGAAGAAGGTATATGCCAAGTGCTAGCTC
ATATGTGGTTGGATTCTGAGATAATGGCCGGTTCTGGTAGTAATATGGCC
TCAACTTCATCAGCATCCTCCTCCTCATCTGCTCCCCCATCATCAAAGAA
GGGAAAGCGTTCTGATTTTGAAAAGAAACTCGGGGAGTTCTTCAAGCATC
AGATTGAATCAGATACCTCAGCAGCCTACGGAGATGGATTCAGAGAGGGT
AACAAGGCAGTGCTCAAGTATGGCCTCAGGAGAACCCTCGATCACATTAG
ACTAACAGGCTGCTTTCCTTAGAAAATCTGCGTCGGTTGCAGCTTACATT
GGACAAACACACACAAACACACACATATGTACACAAGTATATATACCCTG
GCTCTACAAAATTTCAGAATTGCTCAATAGAACAAGAGCAGTATTAGAAT
AAATCATAAGGTGACTGAATAAACAGAAAGTGCTTGTATGTTATGCATAA
TCCATGCACATCTATATTACAGAGAGAAAGAGATAGGAATGTATAACTTT
GCTTTTGCTGTTTTGCACATGACTGTAGCCTATGAAATGCACTCTAAGCA
TATATATGTATCTGAGCAGAATTTTCTTTA