MmuINT0078443 @ mm10
Intron Retention
Gene
ENSMUSG00000004980 | Hnrnpa2b1
Description
heterogeneous nuclear ribonucleoprotein A2/B1 [Source:MGI Symbol;Acc:MGI:104819]
Coordinates
chr6:51466495-51467052:-
Coord C1 exon
chr6:51466906-51467052
Coord A exon
chr6:51466706-51466905
Coord C2 exon
chr6:51466495-51466705
Length
200 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
TAACTTTGTAATTATTGCAGGAG
3' ss Score
6.79
Exon sequences
Seq C1 exon
GTTATGCGGGATCCTGCAAGCAAAAGATCAAGAGGATTTGGCTTTGTAACTTTCTCATCCATGGCCGAGGTTGACGCTGCCATGGCTGCAAGGCCCCATTCCATTGATGGCAGGGTAGTTGAGCCAAAACGTGCTGTAGCAAGAGAG
Seq A exon
GTAAGGAAAACCCAAACACATTGATCTCCTTTCTTGTACTGTTTTTTTTTTTTTTTGTTTTGTTTTTTTTTGGGTACATGTTATTCCAAGACCAACCTCTTAAAACCTATTATCTGGAGGAATTCGTCCTAAGATGTACAAATACAAGTTAGATGTAATCAAGGTTTTTTTCTGTCAGGATAACTTTGTAATTATTGCAG
Seq C2 exon
GAGTCTGGAAAACCAGGAGCCCATGTGACTGTGAAGAAGCTGTTTGTTGGTGGAATTAAGGAAGATACTGAGGAACACCACCTTAGAGATTACTTTGAAGAGTATGGAAAAATTGATACTATTGAAATAATTACCGATAGGCAGTCTGGAAAGAAAAGAGGCTTTGGCTTTGTTACTTTTGATGACCATGATCCTGTGGATAAAATTGTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004980:ENSMUST00000069949:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.245 A=NA C2=0.155
Domain overlap (PFAM):
C1:
PF142591=RRM_6=PD(57.1=81.6)
A:
NA
C2:
PF0007617=RRM_1=PU(81.4=80.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGGATCCTGCAAGCAAAAGA
R:
TCTTTCCAGACTGCCTATCGGT
Band lengths:
295-495
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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