MmuINT0114445 @ mm9
Intron Retention
Gene
ENSMUSG00000022283 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]
Coordinates
chr15:36528707-36529232:-
Coord C1 exon
chr15:36528960-36529232
Coord A exon
chr15:36528798-36528959
Coord C2 exon
chr15:36528707-36528797
Length
162 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GACTTATTTTCTTTACCCAGACT
3' ss Score
6.47
Exon sequences
Seq C1 exon
GTAATGATGGAGGGTGGGCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTCATCCCCTGAAGAAGCCACTAAAGCAGTTACAGAGATGAATGGTAGAATTGTGGCCACGAAGCCACTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGCGCCAGGCTCACCTCACTAACCAGTATATGCAGAGGATGGCAAGTGTACGAGCTGTGCCCAACCCCGTGATCAACCCCTACCAGCCAGCACCTCCTTCAGGTTACTTCATGGCAGCTATCCCACAG
Seq A exon
GTGAGTGTGAAGAAGAAACTAAGTCAGGTTGGCTTCATAAGCTCTCCACGATAAAGCACTAAGTTATTCGATTGGGAAGACAAATGACAAGGGTGGTAGAGTCAGTTGTTTTGAGAGCATGTAATGATAGTTGTGTTTTGTGGACTTATTTTCTTTACCCAG
Seq C2 exon
ACTCAGAACCGTGCTGCATACTATCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022283-Pabpc1:NM_008774:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.308 A=NA C2=0.742
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=42.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATCCCCTGAAGAAGCCACT
R:
GTATGCAGCACGGTTCTGAGT
Band lengths:
246-408
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: