MmuINT0114470 @ mm9
Intron Retention
Gene
ENSMUSG00000011257 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:MGI Symbol;Acc:MGI:2385206]
Coordinates
chr4:122968976-122970202:+
Coord C1 exon
chr4:122968976-122969113
Coord A exon
chr4:122969114-122970106
Coord C2 exon
chr4:122970107-122970202
Length
993 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
AACAGTGATCCTCTCTCCAGGGG
3' ss Score
7.85
Exon sequences
Seq C1 exon
GCTGTGGAAGAAATGAATGGAAAGGAAATGAGCGGGAAAGCCATATTTGTAGGCCGTGCACAGAAAAAGGTAGAAAGGCAGGCTGAGCTGAAGCGGAAGTTTGAGCAGCTCAAGCAGGAGAGGATTAGCCGGTACCAG
Seq A exon
GTGAGGTGGGCTGCTGATTTGAGGGTGTTGATGTGGAATGTTTGACGTGCCTGTGGTATCTTAGGCTTCTGTGGGGGCTGGGCAACCATATTTACCCCCACCCCCGCCTCCACAAAGGTCAGGTTTAAAGGTTGTCACCTACCAAATCATTACAGAGCGGGGGGAGCAGGGACAGTGATGCTCTTTGTGTGAGTACATTCTCCTAAACTGATCCCCCTTCGGAGTAACAACTAAAGAACCCCGTGGGGTGAGTGGCTGGTCCAGCACTTACAGGAAAGGTGTCTGCATCCATCCCTCTGATTGCTCGAGGGCAGGAGTTGCTGATCTTGGTCGGCTTATATCAGAATCCAGCAGAGTTTTTTGTTCTGTTCTGAGACTGAGTTTTACTATTAAGTCAGGGTGGCCTGAAGGAAATCACTGTATCTTAGGCTGACCTGGAACTCTCAGCAGCCCTCCTTCCCTCCAAACAGGAGTGGGGGCCCCAACTCTGGAGCTTCAGGTTTTTTGGTTTTGTATTTTTTAAGATTTACTTACCTATTATATGTAAGTACACTGTGGCTGTCTTCAGACACACACCAGACCAGAAGAGGGAACCAGATCTCGTTACAGATGATTAGACTCAGGAGCTTCAGAAGAGCAGTCAGCGCCCTTCACTGCTGAGCCATCTCTCCAGCTTCTGGTTTTGTGGTTTTAAGTTAGGGTCTTGCTCTGTAGCCTAGGCTGGCCTCAAACACTATTCCCCTGCCTGAGTACAGGGGTTACAGGCAAGAGTTTTTGTTTGATTGGTTTTGGTTTTCCCAGACAGGGTTTCTCAGTGTAGCACTAGCTGGCCTGGAAATCACCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGTGTGCACCAAGCACTGCCTGGCTACAGGCAAGACTTTGAACTTGACAGGTGCCTAAGTATGTTGTTCTTGGGAAGTGACTGTGTATAGAGATGTAGTTAACAGTGATCCTCTCTCCAG
Seq C2 exon
GGGGTGAATCTCTACATTAAGAACTTGGATGACACCATTGATGATGAGAAATTGAGGAGAGAGTTTTCTCCCTTTGGATCAATCACCAGCGCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000011257-Pabpc4:NM_148917:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.109 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(21.4=32.6)
A:
NA
C2:
PF0007617=RRM_1=PU(40.6=87.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGTGGAAGAAATGAATGGAAAGG
R:
GCGCTGGTGATTGATCCAAAG
Band lengths:
230-1223
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: