| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017370340.1, is a part of gene, LOC108201985. |
| The genetic_marker, MK003997 K1441, is located in gene, LOC108201985. |
| 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_017370340.1 | XM_017370340.1 | mRNA | DCARv2_Chr1:46769943..46774717 |
TCATCGTACTGAAAGAGCACACTTAAACTAGAGCTTTGTAAGAGAGAGAT
TGATCGAGAGATTGAGAGAGATGGAACAGAGATCTGGGAACAATGAGTAC
AACCGTGGTGGTGGTGGTGGACGAGGTCGTGGTGGTGGTGGAAGAGGTCG
TGGCGGTGGGAGAGGTGGGGCCCAGGCGGGGTACCAGCAAGGCGGTGGTG
GTGGGAGAGGTGGGGCCCCAATGGGGTACCAGCAAGGTGGGAGAGGAGGT
GGTGGTGGGCGAGGTGGGCCGCCAATGGGGTACAATCAGCAACCGGTTCG
CCCGTGGGAGAACCGGCCGGTTCAAGGTGGACAGCAGCAGGGAGGGATGA
ACCCCCGCCCGGTTCACGGTGGACAAAACCCTCGTCCGGTTCAGGGTGGG
ATGAACCCGCAACCGGGTCAAGCGTGGGGAAACCGTCCGGTTCAGGCTCC
GGTTCATGGTCGGGAAAACCGGCCGGTTCAGGGATGGGCACAGCCGCAGC
AATTTGGTGGGCCATCATCAGTTGAAGCTGCTCCTGAAGATGTTCCTGTG
ACAGGTACTTCTATACAGATCTGTATGTATATAATGTAGGCCCAACCCCT
TACTAATCTTTATCTGTTCTTTACCTATATTCAATTTACTGAATTTTATT
TTTGATTAAAATATCCTATCTTTTACTCCATATTTGATCCATTTTTGTTT
GCATGTGTGGTTGATTGAAGCTAGTAACCTTTTAGATTTTAAAGAATGTC
TTTTAGATATTTATGATTAGTTTCTTCTTTAATGTAATGTAATATCTAAT
CGGAAAAACTATGATGATCAAGATCTGTTTTGAATAGTGGTTTTGGTTGA
GGCTCACCAATATAAAGAGTGTGGATGCAGATATATCTCCTCCCCTCTAA
TTTCTTTACTTTTTATTTCACCGCTCGACCCGCGTTACAAGACTCTTATA
GAATATAGTTCCGTAACTTATTTTTAAGATTTTCTTTTTGTGTATAAAAA
TTCAAACATCAAATTTTTATTCAAAAGAAAAAGATTAAAAAATAAGTTAC
GGAGCTATGTTTTCTTTTTAAAAAATTACAAATAATGGTCTTGAATAGCC
ATTTCTTGTGATATGAAAATAATAATTTGCTGTTTAATATTTTATGATGT
ACAGGTTTTCTTTTTCTTGTTTTTTTTATTTTTTGTGATTTTTGTAGTTT
GAGTAGTTCTATGACAATGTTCATGATAAAACCAGGATGATTCACTCTCG
TGCCATGATTAGGAAAGATCAAGTTTTAGTTAGCCAACTAACTTCAAATG
GACATTTGCATACCCTAGTGTCGTTCTTCACATTGTTTCTTTAGTGGTGT
GATCTTTTTTCTACTGCAGAACTTTGAAATCTGATGCTAGCTATTTGTCA
GTCATGTGTTTTACCTGTTAGAAACCAAGTCTCAGCATTTTTGTTGTTGG
GATAACACTTACCTTTTAGGTACATGAAATTAAAGTTAGGTGATATGTTA
ATGCCTTGCTTGTAACTATGTTATTTTCTAAAATTTCAGGTATGAAATCA
TTGCAAATTTCGGACAGTCCATCTCCTGCCCTTGCTACAACTCCAGGGAA
CAAGCTTCTGCCAATGAGGCGTCCTGATAGAGGGGGCAAAGTTGCAGTTA
GGTCAACCAGGCTTCTTGTCAATCATTTTCCTGTATCTTTCAATCCGCAT
AGCATAATTAAGCACTATGATGTGGATGTTAAGCTGGATGTTGCTCCAGG
GAGTAAGCTTGTAAAGAAACCTGTTCCAAAATCTGAGTTACGGTCAATCC
GAGAAAAGCTATTCGCTGATAGGGCTGAGATATTGCCAATGGACCAAACT
GCATATGACGGTGAGAAGAGCATTTTCAGTGCAGTTGACCTGCCTACAGG
GTCATACAAGGTTGAATTATCTGATGGGGAGGACTCAAAAAGTCGCACAT
ATACATTTACTATTACTCTTGTAAATGAGCTTAAACTGTCTAAACTGAAG
GATTACCTGTGTGGAAACCTTATCCATAAGCCTTCTGAGGTACTAAATGG
AATGGAATTGGTCATGAAGGAGAATCCATCTAGGCAAAGGATCTGTTTTG
GTCGGAACACCTACTCCAGAGAGTATGGGAGAGAGGATGACCTAAAGGGT
GGTCTCGCCGCAAGTAAAGGCTTTCAACAAAGTTTAAAGTCCACATCCCA
GGGACTGGTCCTGTGCCTGGACTACTCAGTTTTAGCATTCCGGAAGCAAT
TACCGGTTTTGGAGTTCCTTACTGAGCACCTGTGTCTCCGAGGGATTAAT
GATATAAACAATTGTAAAAGAGAAGTGCTTAAAGCATTGAAGGGGTTAAA
AGTTACTGTAACTCATCGTCGTACAAAACAGAAATTCACTGTAGCAGGAT
TAACGACAGAAAGCACTCGGAACTTAAAATTCCCTCTTGAGGATCCCGAG
GGAAATGAACCTCCTCGTGAAGTTACCCTGTTAAGTTATTTCCAGGAGAA
ATATGGTATTGATATTAGATACAAAGATATTCCAAGCCTAAATGTGGGGA
AAGGTAAAAGGCAAAACTATATACCTATGGAGTTTTGCGTCTTGGTTGAA
GGACAGAGGTTTCAGAAGGAGAATTTAGATAGAAATGGTGCCATGTTGTT
GAAGAACATATCAGTAGCTTCTCCATTTGATAGAAAGAACAATATCTGCA
GAATGATTAATGCTGGAGATGCACCTTGTGGGTATGTTTTTTAATCTGTT
TTTTTGGTTAAATTTGCCTTTACTTTGTCCAGTCAATTGATTTCTAGTAA
TCTCCTTTGGTATATATGTTAAGTAAAAATTTCAATGAGATTTCTACCCC
GATTTCTGATGTTTGTGTGTTATTTCTCATCTTGGTTGCAGCGGTGACAT
TGTGAAAAATTTTGAAATCGGAGTTAACAAAAACATGACATCAGTAGCAG
GTCGTGTCATTGGGCCTCCTGATTTGAAGCTTGGCACACCAAATGGTCAG
ATGAAAGTGATTAAAGTGGACAGGGAGAAATGCCATTGGAACCTTGTGAG
CAATTCTGTGGTAGAAGGAAAATCACTTGACCGATGGGCTTTATTAGATT
TCAGCTCAGCATCTCGCAGAAATAGGCTGAATCCAGAAAAGTTTGTTTGG
AGTCTTAGAAGCCGATGTGAAAAGTTAGGGATGCATACAGAAGAACCACT
TGCATACCGATCCACAAATATGCAGGCATTTAAAGCTGTGAACAACCTCA
GAGATCTTCTTGGTTATGTGGTTGAGGAGGCTAGTCGAAATAGCAATGGC
CCATTACAATTGATTATCTGTGTGATGGATGGAAAAGATTCTGGTTACAA
GTCCCTTAAATGGGTTTCAGAGACCCAAATTGGGGTAGTAACTCAATGTT
GCTTGTCGGAACATGCTAATGCAGCGAAGGACCAATATCTGGCAAATCTT
GCCATGAAGATAAATGCTAAGATTGGAGGCAGCAATGTAGAGCTCACCGA
GCGGCTTCCCCTTTTAGGAGGTCAAGATCCTGTTATGTTTATCGGTGCAG
ATGTGAATCATCCTGGCGCAATGAATGGGACTTGTCCATCAATCGCAGCA
GTAGTGGGCTCAGTCAATTGGCCAGCAGCTACTCGCTATGCTGCACGAGT
TAGTCCCCAAAGTAATCGCAAGGAGAGAATAGTGAATTTTGGAGGGATGT
GCCTGGATTTGGTTAATTCTTTTGCTAAAATTAACCGAGTAAAACCAAAG
AAGATTATAGTTTTTCGTGATGGAGTAAGTGACAGCCAATTTGATATGGT
TCTAAATGAGGAGTTGCGTGATCTGAAAGCAGCTATATACGAGGAGCACT
ATAAGCCCACAATCACTCTCGTTGTAGCTCAAAAGCGTCATCATACTCGT
CTTTTTCTCGAGGATCAAGGAGGAGATAAACGGCGCAACATCTCCCCAGG
GACGGTTGTGGACACTGTTGTTGTGCACCCATTTGAGTATGATTTCTACC
TGTGCAGCCACTATGGACAACTTGGAACAAGCAAGCCAACTCACTACTAT
GTTCTTTCTGATGACCATAATTTTACATCTGATCAGCTGCAGAAGCTCAT
ATATCAGATGTGCTTCACTTTTGCTCGATGCACTAAACCTGTCTCCCTTG
TGCCACCTGTTTACTATGCTGATCTTGTTGCAACTAGGGGAAGGATGTTT
CAAGAGGCGATGTTGGAGCAGTATCCCCCTTCAAACATGTCATCAAGTTC
TTTGGTATCATCAGCCTCTTCTTCTGCTTCATTTGATGATGCATCGTACA
AGCTTCATGCAGCTCTTCAAGATATCATGTTCTTTATCTGAAGTCTTCAT
TCCCGAGTGAGGCCGTGTGATTTCTTATGCTTTTCATACTGGTTTAGGAA
ATTCATGTCATCACTAAGTCCCTGACGCAGGTCTCCATTCCTATTTTTGC
TAGAAAAGGGGTTTGTGCGCGAATCTAAACGGGTTTTTATAAGTTTGTTT
TGGCATCTTAGTTTTAAAACTTCGTTTGAGTGTTGCATTGCTTCTTGTTT
AGGAGTACTTGGTATCTGCACCAGGTGGTTTCTTGTCTGCAAATGTATTG
TGGGCATGGTACTGTTGAGTGCTGATCAAGTACTGTTTTAACTTCTGTTT
GTGTTGGATTTTGTGTTGAAGTCTATTTCTAAGTTCGTGTGCTATTTATG
TGTTATTCAGTTTTGCTTTGTTATCATGTTTGCTTTGGTTTTTATATTGA
ATGAAATCTGTGTTCAGTGAGCTA