XM_017401365.1

Resource Type: 
mRNA
Name: 
XM_017401365.1
Identifier: 
XM_017401365.1
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_017401365.1
Product: 
probable cyclic nucleotide-gated ion channel 20, chloroplastic, transcript variant X1
Sequence: 
TTGTACCAGCGCTGTAACAATAAACTCATTCAACTGTCCCATCTTAATAC
TCATACATATTCTTGGAATCAGTACAGACACTGATACACACACATATATA
CAGACAGTCAAATTGTAGAAGACCTTTTAGTTCTACATTCCAGCTGCATG
CAGTGTGCAGCTTGAGTAATGGATGCTTCTGACAAAGCTCAGGAATATAT
GAAAACGAATGGAAATGAGAAGCCTAAGTCTAGAAGCTCCACAAATGGAA
TGCGGAGTGCATCAATATCCATTCCGATGTATTCTCTGGATTGCAGTGAT
ACAGAAAATAGTTTCTCAGGTCGTAGTGGTCCGTTGTGTACTGAAAGAAA
AATATCATACACGCAAATGAGTGGTCCTCTTTATGCAAACCTTAAAAATG
ACAACTGTTTTCAAGATACACAAGGTGCAATCGGGAGCAGAGCAACTGAG
GCAACATTGGAGAAGTACCCTTCGGTCAATGGATTGGTTCAAATTGATTG
GCCACATAACAATCATGTGGTAACAAATGAAAATTTATTAAGTTCTGGTC
AACTCGGAATGTGTAATGACCCGTATTGCACAACATGCCCCACTTACTTT
GAAGGGCAGCGAAAGAACAAGAAAGTATCCAGTATATCTGATCAGAAGAA
GCTTCCTTATATCAATTACCAGCAGTTTCCTATCCCTACCATCAAACAGG
GAGATGCAAAAGGCTGGGCATGGAGAATGTTTTTTTCTCTGTATCGATGT
ATTCCGGGAGTCATGAATCCACATGCTAAAATCGTTCAATACTGGAATAA
GTTCTTTGTCATCTCGTGCTTATTTGCGGTTTTTCTAGACCCACTCTTCT
TCTTTTTGCTATCTGTAAAGAAGGAACACAAATGCATAGTATTTAACGAG
ACCATGACAAAAGTTCTTATCACTCTGAGAAGCCTGACTGATTTCATTTA
CTTCTTGCATGTGCTTCTTCAGTTTAGACTGGCGTATGTTGCTCCTGAAT
CAAGAGTTGTGGGTTCTGGTGATCTAGTTGACCGTCCAAGGAAAATAGCT
CTCAATTATCTCTACGGGCACTTTCTTATTGATTTCTTTGTAGTGCTACC
TCTTCCCCAAATAATTATATGGCTGGTACTCAAAAAGTTTAAAGGATCTT
CTGGTGCAAATTATGCAAAAAACTTCTTGCGAGCAGCAATTCTTGTTCAG
TATATTCCGAGGTTGTATAGGATTCTTCCTATGCTTGCTGGTCAGACGGC
AAGCGGCTTTATCTTCGAGTCAGCGTGGGCGAATTTTGTTATCAATCTCC
TCACATTTGTGTTGTCTGGCCATGTGGTTGGGTCATGCTGGTATCTCTTT
GGGTTACAGAGGGTAAATGAATGTCTCAGAAATGCTTGTGATGAGCATTG
GTGTATAAAATTTATAGACTGTGGGCAAGGAAATGAAAATGAGAGGTTCA
GAGATAATCTAGAGTCATGGAAAAATTGGACAAATAATGCCACAGCTAGT
GCTTGTTTTGGTGAAGGCAGTTTTCCATATGGAATTTACGTGCAAACAGT
CAATCTTACCACTGAATCTTCTCTAATTACGAGATACATATATTCATTGT
TCTGGGGTTTCCAGCAAATCAGTACTCTAGCTGGAAACCTTACTCCAAGT
TTCTATGTTGGGGAAGTTCTGTTCACCATGGCCATCATTGGACTCGGTCT
TTTGCTTTTTGCTCTTCTCATTGGTAATATGCAGAACTTTCTACAAGCAC
TTGGTCGCAGGAGACTAGAATTGTCTTTAAGGCGTCGAGATGTTGAGCAG
TGGATGAGCCATAGGCGTCTGCCAGAGGAACTAAGAAGGCAGATCCGTGA
ATCGGAACGTTATAATTGGGCTGCCACTAGAGGGGTTGATGAAAGTATGC
TGTTGGAGAATTTACCTGAAGATCTTCAAAGGGATATACGGCGACATCTC
TTTAAATTTGTAAACAAAGTTCGAATCTTTTCTCTGATGGATGAACCAGT
CTTAGATGCTATGCGTGAGAGACTGAAACAAAAAACATATATCAAAGGAA
GCAGAATTTTAGTTCCCGGAGATCTGGTTGATAAGATGGTATTTATTGTT
CGAGGCAAGCTTGAGAGCGTAGGAGAAGATAAAAATATAGTTCCTTTGTC
TGAAGGGGATGTTTGTGGAGAAGATCTTCTTACCTGGTGCCTTGAGCATT
CTTCTGTAAACAAAGATGGAAAAAGAATCAGGAGTCCAGGACACAAGCTG
CTTAGTAATAGGATGGCAAGATGCTTAACAAATGTAGAAGCTTTTATACT
TCGAGCTGCAGATCTCGAAGAAGTTACTAGTCTTTTCTCTAGGTTCCTGA
GAAATCCACGCGTTCAAGGTGCACTCAGGTATGAATCTCCTTACTGGCGG
TGTCTTGCAGCAACTCGGATTCAAGTTGCATGGAGGTATAGGAAAAAGCG
GTTGAATCGTGCAACAACTGTTAGTTCTACATATAACCATTCCCCAGGAA
ACTAATGATAGTCTATACGCATCATACATGATACATGCATTATAGTTTAG
GTCATCTCGAGCTTGTTTTGTGCGTTAAGCCAATTTATACTATCTATAAT
ATGGGTATAATCTAAATTGCCAACTGAGTACCTCAGCTATGAGGTTGGTG
CACTTTGTATACTTCAACTAGGCAGAAGTAACAGACGTA
Sequence Length: 
2689
Sequence Checksum: 
a12a9509484448cc9d52ab06066c470f
View location in JBrowse: 
DCARv2_Chr6:211287..221428+
Protein Sequence: 
MDASDKAQEYMKTNGNEKPKSRSSTNGMRSASISIPMYSLDCSDTENSFS
GRSGPLCTERKISYTQMSGPLYANLKNDNCFQDTQGAIGSRATEATLEKY
PSVNGLVQIDWPHNNHVVTNENLLSSGQLGMCNDPYCTTCPTYFEGQRKN
KKVSSISDQKKLPYINYQQFPIPTIKQGDAKGWAWRMFFSLYRCIPGVMN
PHAKIVQYWNKFFVISCLFAVFLDPLFFFLLSVKKEHKCIVFNETMTKVL
ITLRSLTDFIYFLHVLLQFRLAYVAPESRVVGSGDLVDRPRKIALNYLYG
HFLIDFFVVLPLPQIIIWLVLKKFKGSSGANYAKNFLRAAILVQYIPRLY
RILPMLAGQTASGFIFESAWANFVINLLTFVLSGHVVGSCWYLFGLQRVN
ECLRNACDEHWCIKFIDCGQGNENERFRDNLESWKNWTNNATASACFGEG
SFPYGIYVQTVNLTTESSLITRYIYSLFWGFQQISTLAGNLTPSFYVGEV
LFTMAIIGLGLLLFALLIGNMQNFLQALGRRRLELSLRRRDVEQWMSHRR
LPEELRRQIRESERYNWAATRGVDESMLLENLPEDLQRDIRRHLFKFVNK
VRIFSLMDEPVLDAMRERLKQKTYIKGSRILVPGDLVDKMVFIVRGKLES
VGEDKNIVPLSEGDVCGEDLLTWCLEHSSVNKDGKRIRSPGHKLLSNRMA
RCLTNVEAFILRAADLEEVTSLFSRFLRNPRVQGALRYESPYWRCLAATR
IQVAWRYRKKRLNRATTVSSTYNHSPGN
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017401365.1, is a part of gene, LOC108226409.
The polypeptide, XM_017401365.1, derives from mRNA, XM_017401365.1.
Cross Reference: 
NCBI Gene
NCBI Nuccore
Gene: 
LOC108226409
Model Evidence: 
Supporting evidence includes similarity to: 6 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
Gbkey: 
mRNA