MmuINT1020339 @ mm10
Intron Retention
Gene
ENSMUSG00000056116 | H2-T22
Description
histocompatibility 2, T region locus 22 [Source:MGI Symbol;Acc:MGI:95956]
Coordinates
chr17:36038409-36039054:-
Coord C1 exon
chr17:36038985-36039054
Coord A exon
chr17:36038777-36038984
Coord C2 exon
chr17:36038409-36038776
Length
208 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTGT
5' ss Score
7.44
3' ss Seq
TTCCTTTTATATCCCATCAGTTG
3' ss Score
7.08
Exon sequences
Seq C1 exon
GAGATGGGGGTTTGCTTTTGGAAGATTAAGTCCTGTAAAACTTGTCTAGGCCACTCCCCAGGAACTTCAG
Seq A exon
GTTTGTTTACCATGTCACCCCGAAAGAGGTATCAGCCTGTCTTCCCCACCCCACCCCCAACTCTGTCGGTGTTGTCTCCCAGAAGGCTTCACTTAGCCTCCTCACCCTCCAGAGAACACTCCCAGCTGTTCCCCCTCACCCACCGCCTCTGTGGGATCACCTGCAACAGTTACTGAAGAATGCAATCTTTCCTTTTATATCCCATCAG
Seq C2 exon
TTGGCGAGTCTTTACTGTCACCTTGACTGGATTTAGGATCATCTGGGAGATGCCCCTTTGAGTGGCTGGGCTGTGAGGACAGCAGGCCAGTTCTTGCCACCCTGGACAGAAACACATCTCACCTTTCTGGCTCAAGGATCTGAACACCTGTCTCTTGCCTACTCGGCTTCTAGTCAGGCATTTTGTCACCTTGTCAAGGGTCCCAGGGACACAAAGCTCCCTCCTCTCACCCACAGCACTCTGGGTCCTACCCTCAGTGCTTCAGGGACATTTAATCAGGTCAAATTGGGATCAATGGCTTTGATGCAGAAAAGAACTGTGGACTAATAGAGATAGGGTTTAATTAAAAAATATATCTTTTTAATTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056116:ENSMUST00000080015:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.107
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACTTGTCTAGGCCACTCCCC
R:
CCTGAAGCACTGAGGGTAGGA
Band lengths:
298-506
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types