HsaINT0113813 @ hg19
Intron Retention
Gene
ENSG00000114857 | NKTR
Description
natural killer-tumor recognition sequence [Source:HGNC Symbol;Acc:7833]
Coordinates
chr3:42672663-42674315:+
Coord C1 exon
chr3:42672663-42672808
Coord A exon
chr3:42672809-42674092
Coord C2 exon
chr3:42674093-42674315
Length
1284 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
TTATTAATGTTTCTTAAAAGTTT
3' ss Score
7.11
Exon sequences
Seq C1 exon
GGTGCATGTAGTCTTTGGACTGGTTATTTCTGGTTTTGAAGTAATCGAACAAATTGAAAATCTGAAGACCGATGCTGCAAGCAGACCATATGCAGATGTGCGAGTTATTGACTGTGGAGTACTTGCCACAAAATCAATAAAAGATG
Seq A exon
GTAAGAACTTTTTTGACAGTAGATGAAGCTAAGATGCAGGTAAAGCATTGCTGAAGACTGTAACTAGATTTGATTAGTGGAACTAGTGGTATAGCAATAGCCCTTGGTGCCCCTGAATCATACCCTACATGTTTAATCTTTTAGCATATCTTGTCAGATCTTACTTTTTCTTATTTCCTTGCCACCAGCCTTATCCACACCACCAGTATTTTGTGTCTGGATTATTGCCGTAGCGTCGTAACTGTTTACCTTGCCTCCGTTCTATAATCTTTTGTCAGCAGCAATAGCCTCCTAACTGGTCTCATTGCTTATATCCTAGGCCCGCTGTGGTCTGTCCTTAACAGCAACCAGAGTGATCCCTTTGAACCATAGTTTGCATTCATGTCACGCCTGCACAGAACCCTCCAAGGACTCCCATCTTCAATCATCCAAAGCAGAAGTCTTTATGGTGGTCTCTAAGGCCCTGGCTGGTCTGGCTCTCTGCTGTCTCTCTAAACTCTTTTCCCTTATTCATTGCCTTCCAGGCACATTGACCTTTTTTCAGACATGCCAACCACTCAGGGATTTTGTGCTGCCTATTCTCTTTGTCTGGAACACCCTTTGTTAAGATATCTGCATGACACTGTCCCTTGCTCTTAAGTCTCTGTTCAAATGTTATGTTAAACTACCCCTAGTCTTCCTATTCCCTTTACACTGCTTTGTTTTTCTGTCTTAGCACTTAATCATTTGTCATATTATGCAATTCTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAAGAGTCTTGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACTATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAGGTGATTCTCCTGCCTCAGCCTCTGGAGTAGCTGGGATTATAGGGATGCACCACCATGCCTGGCTAATTTTTGTTATTTTTAGTAGAGACATGGTTTCACCATGTTGGCCAGGCTGGTCTTGTACTCCTGACCTCAAGTGATTTGCTCACCTTGGCCTCCCACAGTGTTAGGATTACAGATATGAGTCACTGCACCGGGCCTATTTCTTGTTACTTGACCCAACAAGAATATAGGCTTCATAAAGACAAGGGACTTACTACCTTACAATCTTGCCAGTAATTTTATTATAAACTTGAAAAAAACTGTCTACATTTCATTTTTTGTTTGCTGTATGTAAAGCATATTTTATGATATTCAGTAATCACATTTTTTACTCTGAAAGGTAGGCACTGAATTTAGTACTAATGTTTTTATTAATGTTTCTTAAAAG
Seq C2 exon
TTTTTGAGAAAAAAAGGAAGAAACCAACTCATTCAGAAGGCTCGGATTCCTCTTCCAATTCCTCCTCTTCTTCAGAATCATCTTCAGAAAGTGAACTTGAACATGAGAGAAGCAGAAGGAGGAAACATAAGAGGAGGCCAAAAGTTAAACGTTCTAAAAAGAGGCGAAAGGAAGCAAGCAGTTCAGAAGAGCCAAGGAATAAACATGCAATGAACCCAAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114857-NKTR:NM_005385:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.016 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0016016=Pro_isomerase=PD(24.1=80.0),PF105004=SR-25=PU(17.3=56.0)
A:
NA
C2:
PF105004=SR-25=FE(45.7=100)
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:
TCTTTGGACTGGTTATTTCTGGT
R:
CCTTTTGGGTTCATTGCATGT
Band lengths:
358-1642
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)