HsaINT0113808 @ hg19
Intron Retention
Gene
ENSG00000114857 | NKTR
Description
natural killer-tumor recognition sequence [Source:HGNC Symbol;Acc:7833]
Coordinates
chr3:42659062-42660619:+
Coord C1 exon
chr3:42659062-42659136
Coord A exon
chr3:42659137-42660511
Coord C2 exon
chr3:42660512-42660619
Length
1375 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TTTTTTTTTTTTTTTTCCAGGAG
3' ss Score
12.13
Exon sequences
Seq C1 exon
TTGGTCGCATTATGTTTCAGCTCTTCTCAGACATATGTCCAAAAACATGCAAAAACTTCCTTTGCTTGTGCTCAG
Seq A exon
GTAAGTGAATTATTATTTCCAATGAGAAGCTGTGGCTTACAGTTTTACCTTGCTGAACAGAATAGATATTTTCCTGGAAGAATAATGGACTCGTGAAATTAGTTTTGTGAATTAAAAAAAAAAAAGAGTTACTTATACTGACTTTTATATGAAATCAGGGAAGCATTTCTTAAGGGGAAGAGATTAGAAAGGAATGATCTCAAAAATGAAAAAGAGAGTAAGAATCTACGTTATATAATGGAATCTTCTCTATACATTTTAATTTATAAAATAATAGCACACATTCAAAACTGATTTGGTAGAATTTTATGAATTTCACTACTTTGAAAAAATTTAGTATTCCAAATTTTACAATAAATTTTAAATAAATAGAAAAAATGGGGAGGGAAACATCTATAATGTTACTTTAAAATTAGAACAAACTGGCCGGGTGCGGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGAGTTCAAGACTAGCCTCGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTAGTGGCAGGCGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAAGAGAATCACTTGAACCCGGGAGGCGGAGCTTGCAATGAGCCAAGATTGCGCCATTGCACTCCAGCCTGGGGGACAAGAGCCAGACTTTGTCTCAAAAAAAAAAAAAAAAAAATTAGAACACACTGAAATTTTAAATTCTTACTTGGATACACATATGCAATTTTTGCACTAACTCCTTGATTTTGTTATTTATTTATTTGGGACGGAGTCTGACTCTTGTCTCAAAAACAGGCTGGAGTGCGGTAGTGTGATCTCAGCTCACTGCAACCTCCACCTCCCAGATTCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGCCTGTGCCACCACACCTGGCTAATTTTTGTATTTTTTTTTTTAGAGGCAGAATTTCACCCTGTTGGCCAAGCTGATTTCAAACTCCTGACCTCAAGTGATCTGCCTCGGCCTCCCAAAATGTTGGGATTACAGGCGTGTGCCATTGCGCCTGACCTCATTCTTTGACTAGAGTGATAAGTGTGTCTAGTATTATGTCCTATAGCATGTAGAGTCTGTACCACACAATTTTACATTTACATGCTGCTTTGGATTATTTATTTTGGTTTGCGTGCATGTGTGTATGTTAAATTATCATGTCATCTATTTCTTATATCTCTTCCAGTGCCTAGCACACAGGAAAGATTTGACACAGGATTAATTGGTTTGTTCTTTCCATGGAAGGATGTATAAATAATTAAACTTCATTTCTTTTTTTTTTTTTTTTTTCCAG
Seq C2 exon
GAGAGAAAGGCCTTGGGAAAACAACTGGGAAGAAGTTATGTTATAAAGGTTCTACGTTCCATCGTGTGGTTAAAAACTTTATGATTCAGGGTGGGGACTTCAGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114857-NKTR:NM_005385:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0016016=Pro_isomerase=FE(26.6=100),PF132061=VSG_B=PU(19.7=46.2)
A:
NA
C2:
PF0016016=Pro_isomerase=FE(27.3=100),PF132061=VSG_B=PD(68.3=75.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTCGCATTATGTTTCAGCTCT
R:
CTTCACTGAAGTCCCCACCCT
Band lengths:
182-1557
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)