XM_017391613.1

Resource Type: 
mRNA
Name: 
XM_017391613.1
Identifier: 
XM_017391613.1
Organism: 
Daucus carota subspecies sativus
Analysis: 
NameDescription
Carrot Genome Assembly DCARv2

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
Authors' original naming scheme: Sequences with DCARv2 prefix are the original assembly as submitted to NCBI. These are labelled DCARv2_Chr1 through DCARv2_Chr9 for the chromosome pseudomolecules, DCARv2_MT and DCARv2_PT for the organellar assemblies, DCARv2_B1 and up for unincorporated superscaffolds, DCARv2_S26.1 and up for unincorporated scaffolds, and DCARv2_C10542132 and up for unincorporated contigs. A file with sequences using this naming scheme can be downloaded from the File: link below.
These sequences can be viewed in JBrowse here.

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
NCBI Daucus carota subsp. sativus Annotation Release 100

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 Id: 
XM_017391613.1
Product: 
putative DEAD-box ATP-dependent RNA helicase 29
Sequence: 
TGTTCATTAAGGGTTTAAGAAATTAAACAAAACCCTCGACCCGCTCCTAT
TCTTGCCAGACCTAACCGTCTCTCTCCTCTTTCTTCAACGTCCATCTATA
CACACAAATCCCTGTATCTATCCTTCACCACTCTCATTCAACCTGTAAAA
ACCTCCAATTCATCAATGGACTACGAAGCTCCACTCCTTGTAAGCTCCGT
AACGGAGCTCAAAAAGAAGGAAAAGCTCCAAAAGAAAGCCAAATCAGGCG
GATTCGAGTCATTAGGGTTAAGTTTCAATGTGTTTAGAGGCGTTAAACGG
AAGGGATACAAGGTGCCGACGCCGATTCAGCGCAAAACGATGCCGCTTAT
ACTCTCTGGCTGCGATGTTGTGGCCATGGCTCGGACTGGTTCCGGCAAAA
CGGCGGCGGTTTTGGTGCCGATGTTCGAGAAGTTGCGGAATCATTTGGAT
GAGTGCGGTGGGATTCGGGCTTTGATTTTGTCGCCGACGAGGGATTTGGC
GCTTCAGACTCTTAAATTTGCTCAGGAATTGGGTCGATATACCGATCTTC
GAATTAGTTTATTAGTAGGAGGCGATAGTATGGAAAGTCAGTTTGAAGAG
TTGGCACAGAACCCCGATATCATTATTGCAACCCCTGGTAGACTCATGCA
CCATTTGTCTGAGGTTGAAGATATGTCACTGCGTAGTGTGGAGTATGTGG
TTTTTGATGAAGCTGACTGTATCTTTAGCATGGGGTTTGCTGAGCAGCTG
CATCAAATTCTGTCCAAACTTAGTGACAATCGTCAAACCTTGCTCTTCAG
TGCAACTTTACCAAGTGCCCTTGCCGAATTTGCCAAAGCTGGTTTACGAG
ATCCCCAGCGTGTGCGACTTGATTTGGAGACTAAGATTAGCCCTGACTTG
AAGCTTGTCTTTTTCACTTTAAGGCAGGAAGAAAAACATGCTGCATTGTT
GTACTTAATTGAGGAGAGGATTAGACCTGATGAACAGACTTTGATCTTTG
TTTCCACAAAATATCACGTTGAGTTTCTTAATGTTCTCTGTCAAGAAAGG
GGTATTCGTCCATCTGTTTGCTATGGTGATATGGACCAAGATGCTCGCAA
GATGGCTGTATCCCAATTTAGATCAAGAAAGACTATGCTGCTGATCGTGA
CTGATGTAGCAGCCAGGGGGATTGACATTCCTCTGCTTGATAATGTCATC
AACTGGGATTTTCCTCCTAGACCTAAGCTTTTTGTCCATCGAGTAGGACG
AGCTGCAAGGGCTGGTCGGACTGGTACTGCATTTTCTTTTGTCACAACTG
AAGATATGCCCCATGTTTTAGATCTTCATCTCTTTCTTTCAAAGCCTGTC
AGGGCTGCTCCCACTGAGGAAGAGGTTTCACATAATGTGAATAATCTCAT
GTCTAAAATTGATCAAGCAATTGCCAACGGAGAAACCGTTTATGGGCGCT
TCCCTCAGACAGTTCTTGATCTCTACGCAGATAGGGTTCGGGAGTTACTG
GATTCTTCTACCGAATTACATTCATTGGAGAGGCCGTGTACTAAAGCATT
TCGTTTATATTACAAGACGAAAGCAAAGCCTTCTAAGGAGTCTGTTAGAA
GAGCAAAGAAGTTGCCCCGTGAAGGACTTCATCCAATATTCAAAAGTTCG
CTAGGTGGTGATGAGATAACTGCACTTGCCTATCTTGAGCAGTTGAAAAA
ATACAGACCCAAGCAGACTATCTTGGAAGCTGAAGGTGAAGTTGCTAAAT
CAAAGAAAGTAAAAGGGTCTGCAAGTCAAGGGGGTGATGTAATGAAAATG
AAAAGAGCTGTGCATGAGGAGATCATTAATAAAGAACATCAGAAACACTC
CAGAGAGTGTGCAGAAAAGAAATATGAAATGGATGATGATATGGATGAAG
TTATGGAAAACGTTCCTACAGCTGGCATTGAAAAGAAAGTTTCTGGTTCT
AAAAGGAAGGCAAAGAGCTTCAAGGATGAGGAGTACTTCATAAGTTCCGT
GCCAACAAACCAACATTATGAGGCAGGACTTTCAGAAAAGGGCAGCAGAG
GGTTTGAATCTAATAGGTTAGATGCTGATGTTCTGGATCTAGCTGCGGAT
GATAATAGTGGGCTGCAGAAACAAAAGGCATCATATCACTGGGACAAGAG
AAGTAAGAAATACATCAAGCTAAACAGTGGGGACCGTGTAACAGCTAGTG
GAAAGGTGAAGACTGAAAGTGGCGCAAAAGTCAAAGCTAATAAGACTGGG
ATATACAAAAGATGGAAAGAAAGGTCACACAATACAATATCTTCCCGAGG
AACAAGTCGTGATGGCGGTGCTGAAGAACCTACGAATATTGCAGGTGCTC
GGGGGCGTATGGATAGCAGAAGGTTTAAAGGTGGAAAACAACGGCAGTCT
ATACCTAATGCTCATGTGCGTTCGGAATTGAAAAACAATGAACAAGTTCG
GAAGGAAAGGCAAAAGAAAGCAACCAAGCTTCAACAATTAAAGAGTAATC
CCAAGAGGGGTAAAAAATTTGGTAAAGGGGGGAAAAATGGCAAGAGAGGA
GGAAAGTCAAGGTAATTGAACACGAGAGACTTGGTTGTTTTGCTCCCTCT
GTGCTCCGGGGGTAACAAATTTTTTTTGAAGATGTAACAAGTTACTTGAA
AAATATACATTTTTAAACTGAGA
Sequence Length: 
2673
Sequence Checksum: 
c5ede32c7daef4954b5fe12e273c3b6a
View location in JBrowse: 
DCARv2_Chr4:22165248..22182153+
Protein Sequence: 
MDYEAPLLVSSVTELKKKEKLQKKAKSGGFESLGLSFNVFRGVKRKGYKV
PTPIQRKTMPLILSGCDVVAMARTGSGKTAAVLVPMFEKLRNHLDECGGI
RALILSPTRDLALQTLKFAQELGRYTDLRISLLVGGDSMESQFEELAQNP
DIIIATPGRLMHHLSEVEDMSLRSVEYVVFDEADCIFSMGFAEQLHQILS
KLSDNRQTLLFSATLPSALAEFAKAGLRDPQRVRLDLETKISPDLKLVFF
TLRQEEKHAALLYLIEERIRPDEQTLIFVSTKYHVEFLNVLCQERGIRPS
VCYGDMDQDARKMAVSQFRSRKTMLLIVTDVAARGIDIPLLDNVINWDFP
PRPKLFVHRVGRAARAGRTGTAFSFVTTEDMPHVLDLHLFLSKPVRAAPT
EEEVSHNVNNLMSKIDQAIANGETVYGRFPQTVLDLYADRVRELLDSSTE
LHSLERPCTKAFRLYYKTKAKPSKESVRRAKKLPREGLHPIFKSSLGGDE
ITALAYLEQLKKYRPKQTILEAEGEVAKSKKVKGSASQGGDVMKMKRAVH
EEIINKEHQKHSRECAEKKYEMDDDMDEVMENVPTAGIEKKVSGSKRKAK
SFKDEEYFISSVPTNQHYEAGLSEKGSRGFESNRLDADVLDLAADDNSGL
QKQKASYHWDKRSKKYIKLNSGDRVTASGKVKTESGAKVKANKTGIYKRW
KERSHNTISSRGTSRDGGAEEPTNIAGARGRMDSRRFKGGKQRQSIPNAH
VRSELKNNEQVRKERQKKATKLQQLKSNPKRGKKFGKGGKNGKRGGKSR
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017391613.1, is a part of gene, LOC108218606.
The polypeptide, XM_017391613.1, derives from mRNA, XM_017391613.1.
Cross Reference: 
NCBI Gene
NCBI Nuccore
Gene: 
LOC108218606
Model Evidence: 
Supporting evidence includes similarity to: 3 ESTs, 6 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 27 samples with support for all annotated introns
Gbkey: 
mRNA