Special

MmuEX0023089 @ mm9

Exon Skipping

Gene
ENSMUSG00000004980 | Hnrnpa2b1
Description
heterogeneous nuclear ribonucleoprotein A2/B1 [Source:MGI Symbol;Acc:MGI:104819]
Coordinates
chr6:51417184-51419893:-
Coord C1 exon
chr6:51419670-51419893
Coord A exon
chr6:51417390-51417425
Coord C2 exon
chr6:51417184-51417294
Length
36 bp
Sequences
Splice sites
3' ss Seq
GTTTTTTTTCTCCCCCCCAGAAA
3' ss Score
11.41
5' ss Seq
AAGGTACTC
5' ss Score
7.46
Exon sequences
Seq C1 exon
GTTAGTGGGGGGAAGGTTCTAGAAAAGCGGCGGTCTCGGCTCCAGCGGCAGTAGCAGCGGCGCCGGTCCCGTGTGCAGGAGCTCCTTTGCGGCCCAGTTTCTTGGCCATCGCCTGCTCTCCCCACAGCGCCAGGACGAGTCCCGTGCGCGTCCGTCCGCGGAGGTCTTTCTCATCTCGCTCGGCTGCGGGAAATCGGGCTGAAGCGACTGAGTCCGCGATGGAG
Seq A exon
AAAACTTTAGAAACTGTTCCTTTGGAGAGGAAAAAG
Seq C2 exon
AGAGAAAAGGAACAGTTCCGAAAGCTCTTTATTGGTGGCTTAAGCTTTGAAACCACAGAAGAAAGTTTGAGAAACTACTATGAGCAATGGGGAAAGCTCACAGACTGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004980_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (No Ref)

Show structural model
Features
Disorder rate (Iupred):
  C1=0.167 A=0.840 C2=0.000
Domain overlap (PFAM):

C1:
NO
A:
NO
C2:
PF142591=RRM_6=PU(40.0=75.7)


Main Inclusion Isoform:


Main Skipping Isoform:


Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGAAGCGACTGAGTCCGC
R:
GTGAGCTTTCCCCATTGCTCA
Band lengths:
127-163
Functional annotations
There are 1 annotated functions for this event
PMID: 20406423
The inclusion of exon 2 (HsaEX0030279) and exon 9 (HsaEX0030282) generates a predominantly nuclear form, skipping of the exons generates cytosolic forms. The study shows, using isoform-specific antibodies and isoform-specific green fluorescent protein (GFP)-fusion expression constructs, that A2b is the predominant cytoplasmic isoform in neural cells, suggesting that it may play a key role in mRNA trafficking. The differential subcellular distribution patterns of the individual isoforms are determined by the presence or absence of alternative exons that also affect their dynamic behavior in different cellular compartments, as measured by fluorescence correlation spectroscopy. Expression of A2b is also differentially regulated with age, species and cellular development. Furthermore, coinjection of isoform-specific antibodies and labeled RNA into live oligodendrocytes shows that the assembly of RNA granules is impaired by blockade of A2b function. These findings suggest that neural cells modulate mRNA trafficking by regulating alternative splicing of hnRNP A2/B1 and controlling expression levels of A2b, which may be the predominant mediator of cytoplasmic-trafficking functions. B1: inclusion of both. A2: skipping of ex 2. B1b: skipping of ex 9. A2b: skipping of both. Not well in VTS in hg38 nor mm10.


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Pre-implantation embryo development
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types