MmuINT0114436 @ mm9
Intron Retention
Gene
ENSMUSG00000022283 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]
Coordinates
chr15:36526719-36527296:-
Coord C1 exon
chr15:36527212-36527296
Coord A exon
chr15:36526850-36527211
Coord C2 exon
chr15:36526719-36526849
Length
362 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
TAGAGTGTCTGTTGTTCTAGGTG
3' ss Score
6.86
Exon sequences
Seq C1 exon
CCTGCTGTTCATGTGCAAGGTCAAGAACCTTTAACTGCTTCCATGTTGGCATCTGCGCCCCCGCAAGAGCAGAAGCAAATGTTGG
Seq A exon
GTAAGTAACTTTGTTGTCTTGGTCTGTCAGTTAGAGTTGACGAAAATAACAAGGACCACTTAGACACTTTGCACCTAAAATGAGATGGCTTAGGATGGTATGTGAAGGAATACTAGAAAACATGGTGGGCTACTGTTTGCCATTGACATTCCACTCTAGCCTTGAAACAAAGAAGCATTGTCTATGTTAATACCAAACACTTGAGGAACTGATACCACCAGAGAAGTGACTGCCTTGTGACAGATTGTGCTATACATACGGGTGTGGTAGCTAGTACATACTCTATATTAAATAAGGTAGGTTCCTAAACCCCTGGTTGATAATAGCCATTGCCACTCTGATTAGAGTGTCTGTTGTTCTAG
Seq C2 exon
GTGAACGGCTGTTTCCTCTTATCCAAGCCATGCACCCTTCTCTTGCTGGTAAAATCACTGGCATGCTGTTGGAGATTGATAACTCAGAATTACTTCACATGCTCGAGTCTCCAGAGTCTCTCCGCTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022283-Pabpc1:NM_008774:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.966 A=NA C2=0.284
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(27.8=69.0)
A:
NA
C2:
PF0065813=PABP=FE(59.7=100),PF085466=ApbA_C=PU(56.2=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGCTGTTCATGTGCAAGGT
R:
TTGAGCGGAGAGACTCTGGAG
Band lengths:
214-576
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: