Dioscorea cayenensis subsp. rotundata cultivar TDr96_F1 chromosome 23, TDr96_F1_v2_PseudoChromosome.rev07_lg8_w22 25.fasta, whole genome shotgun sequence.
type: Entry
definition: Dioscorea cayenensis subsp. rotundata cultivar TDr96_F1 chromosome 23, TDr96_F1_v2_PseudoChromosome.rev07_lg8_w22 25.fasta, whole genome shotgun sequence.
sequence version: NC_052493.1
sequence date: 2021-02-02
sequence: sequence
division: CON
label: NC_052493.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA695139
dblink: SAMD00039982
keyword: WGS
keyword: RefSeq
source: Dioscorea cayenensis subsp. rotundata (Guinea yam)
organism: Dioscorea cayenensis subsp. rotundata
taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Dioscoreales; Dioscoreaceae; Dioscorea.
comment: REFSEQ INFORMATION: The reference sequence is identical to\nBLBR01000023.1.\nAssembly name: TDr96_F1_v2_PseudoChromosome.rev07_lg8_w22 25.fasta\nThe genomic sequence for this RefSeq record is from the\nwhole-genome assembly released by the Genetics and Breeding, Iwate\nBiotechnology Research Center on 2019/11/25. The original\nwhole-genome shotgun project has the accession BLBR00000000.1.\n\n##Genome-Assembly-Data-START##\nAssembly Provider :: Genetics and Breeding, Iwate Biotechnology\n Research Center\nAssembly Method :: flye v. 2.4.2; pilon v. 1.23; Purge\n Haplotigs v. 1.0.4; MSTmap\nAssembly Name :: TDr96_F1_v2_PseudoChromosome.rev07_lg8_w22\n 25.fasta\nGenome Coverage :: 34x\nSequencing Technology :: Nanopore PromethION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI\nAnnotation Status :: Full annotation\nAnnotation Name :: Dioscorea cayenensis subsp.\n rotundata Annotation Release 100\nAnnotation Version :: 100\nAnnotation Pipeline :: NCBI eukaryotic genome annotation\n pipeline\nAnnotation Software Version :: 8.5\nAnnotation Method :: Best-placed RefSeq; Gnomon\nFeatures Annotated :: Gene; mRNA; CDS; ncRNA\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000340
sequence length: 86346
topology: linear
so has quality: SO_0000987
location: 1..86346
location: region:1-86346:1
RO_0002162: 55577

NC_052493
type: RefSeq
SIO_000068: refseq

PRJNA695139
type: BioProject
SIO_000068: bioproject

SAMD00039982
type: BioSample
SIO_000068: biosample

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:86346:1
position: 86346
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-86346:1:source
so part of: sequence
organism: Dioscorea cayenensis subsp. rotundata
mol type: genomic DNA
cultivar: TDr96_F1
sub species: rotundata
chromosome: 23
country: Japan:Iwate
collection date: 2016-06-01

55577
type: Taxonomy
SIO_000068: taxonomy

LOC120252769
type: Gene
subclass of: SO_0000704
RO_0002162: 55577
gene: LOC120252769
note: Derived by automated computational analysis using gene prediction method: Gnomon.
so part of: sequence
location: 22210..35759
location: region:22210-35759:1
so has part: feature:22210-35759:1:exon
subclass of: SO_0000010

120252769
type: Gene
SIO_000068: ncbigene

position:22210:1
position: 22210
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:35759:1
position: 35759
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:22210-35759:1:exon

LOC120252769
type: Messenger RNA
subclass of: SO_0000234
RO_0002162: 55577
gene: LOC120252769
product: MADS-box protein SOC1-like
note: Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 57 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 15 samples with support for all annotated introns
transcript id: XM_039260919.1
SIO_010081: LOC120252769
subclass of: SO_0000673
so part of: LOC120252769
location: join(22210..22315,22446..22627,34213..34294,34858..34919,35000..35099,35184..35225,35302..35343,35420..35759)
location: region:22210-35759:1
so has part: feature:22210-22315:1:exon
so has part: feature:22446-22627:1:exon
so has part: feature:34213-34294:1:exon
so has part: feature:34858-34919:1:exon
so has part: feature:35000-35099:1:exon
so has part: feature:35184-35225:1:exon
so has part: feature:35302-35343:1:exon
so has part: feature:35420-35759:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:22210-22315:1:exon

position:22315:1
position: 22315
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:22446-22627:1:exon

position:22446:1
position: 22446
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:22627:1
position: 22627
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 3
SIO_000628: feature:34213-34294:1:exon

position:34213:1
position: 34213
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:34294:1
position: 34294
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 4
SIO_000628: feature:34858-34919:1:exon

position:34858:1
position: 34858
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:34919:1
position: 34919
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 5
SIO_000628: feature:35000-35099:1:exon

position:35000:1
position: 35000
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:35099:1
position: 35099
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 6
SIO_000628: feature:35184-35225:1:exon

position:35184:1
position: 35184
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:35225:1
position: 35225
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 7
SIO_000628: feature:35302-35343:1:exon

position:35302:1
position: 35302
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:35343:1
position: 35343
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 8
SIO_000628: feature:35420-35759:1:exon

position:35420:1
position: 35420
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

LOC120252769
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 55577
gene: LOC120252769
note: Derived by automated computational analysis using gene prediction method: Gnomon.
codon start: 1
product: MADS-box protein SOC1-like
translation: MGRGKTEMRRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIVFSPRGKLYEFASSSMQETINRYMAHSKNINIEKRMPEQNAQQLKLEVAAMAKKIELLEGYKRKLLGESLGSCSMFELHEIESQLEKSLTIIRGKKHHMLAEQIAELKEKEKTLTEENLVLRHKAEFSLELNENREFVENDETGEEDIEVETELFIGRPGSRRQCNINA
SIO_010081: LOC120252769
subclass of: SO_0000673
so part of: LOC120252769
location: join(22446..22627,34213..34294,34858..34919,35000..35099,35184..35225,35302..35343,35420..35557)
location: region:22446-35557:1
so has part: feature:22446-22627:1:exon
so has part: feature:34213-34294:1:exon
so has part: feature:34858-34919:1:exon
so has part: feature:35000-35099:1:exon
so has part: feature:35184-35225:1:exon
so has part: feature:35302-35343:1:exon
so has part: feature:35420-35557:1:exon

XP_039116853.1
type: Protein
SIO_000068: ncbiprotein

position:35557:1
position: 35557
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:22446-22627:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:34213-34294:1:exon

urn:…
SIO_000300: 3
SIO_000628: feature:34858-34919:1:exon

urn:…
SIO_000300: 4
SIO_000628: feature:35000-35099:1:exon

urn:…
SIO_000300: 5
SIO_000628: feature:35184-35225:1:exon

urn:…
SIO_000300: 6
SIO_000628: feature:35302-35343:1:exon

urn:…
SIO_000300: 7
SIO_000628: feature:35420-35557:1:exon

LOC120252770
type: Gene
subclass of: SO_0000704
RO_0002162: 55577
gene: LOC120252770
note: Derived by automated computational analysis using gene prediction method: Gnomon.
so part of: sequence
location: complement(66975..69097)
location: region:66975-69097:-1
so has part: feature:66975-69097:-1:exon
subclass of: SO_0000011

120252770
type: Gene
SIO_000068: ncbigene

position:66975:-1
position: 66975
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:69097:-1
position: 69097
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:66975-69097:-1:exon

LOC120252770
type: Non Coding RNA
subclass of: SO_0000655
RO_0002162: 55577
nc RNA class: lncRNA
gene: LOC120252770
product: uncharacterized LOC120252770
note: Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
transcript id: XR_005534132.1
SIO_010081: LOC120252770
subclass of: SO_0000673
so part of: LOC120252770
location: complement(join(66975..67133,68317..68372,69057..69097))
location: region:66975-69097:-1
so has part: feature:69057-69097:-1:exon
so has part: feature:68317-68372:-1:exon
so has part: feature:66975-67133:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:69057-69097:-1:exon

position:69057:-1
position: 69057
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:68317-68372:-1:exon

position:68317:-1
position: 68317
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:68372:-1
position: 68372
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 3
SIO_000628: feature:66975-67133:-1:exon

position:67133:-1
position: 67133
reference: sequence
type: ReverseStrandPosition
type: ExactPosition