MmuINT1026160 @ mm10
Intron Retention
Gene
ENSMUSG00000011257 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:MGI Symbol;Acc:MGI:2385206]
Coordinates
chr4:123288959-123290338:+
Coord C1 exon
chr4:123288959-123289074
Coord A exon
chr4:123289075-123290198
Coord C2 exon
chr4:123290199-123290338
Length
1124 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
CTATCCGTGGTTTCTCGTAGGTT
3' ss Score
8.57
Exon sequences
Seq C1 exon
GTGGTCTGTGATGAGAACGGCTCTAAGGGCTATGCTTTTGTTCACTTCGAGACCCAAGAGGCCGCCGACAAGGCCATCGAGAAGATGAATGGCATGCTTCTCAATGACCGTAAAGT
Seq A exon
GTGAGTGTCCCAGTCTGGAGCAACAACCATCGCATGAGCCAGCCATGGCCCCACCTCGGTATTAACTGGCACACACAAGGCGGCTACTGGTTCTCTCGGCCCAAGTGTGGCCTGCTCCTACCTCTCCACTCCAGGGCTGGTGAGTCTCCCTGCCCGAGCCACGGCAGCCCTTTTGACTTGCCACAGTCGGCTCCCTGCCCGAGCCATGGCCTGCCTGCTGCCTCTCCCTTAAGGCATTCATCTGTGGGTTTTGTGAGCATCGGCAAGTGGGGCTGGCTAGGAGAGCGCTCTGAGCCCACTCTGAGCAGGGGTCTTGGCCAGCGGCAGAGTGGAGAGGCCCTGGGCTGACCAGGAGCTGGATATTGGCTACACAAACTCAGCTTTCTTTCCTTTGACTCATTGCTGCCCGTGGGGCTCTTGCTAGTTTTTGGCACCAAATTGTCCTCTAGTTCTTTTCCTCCGAACTGCAACAACATTTCACTGTCATCCATTTAATTGGCCTACGATGAAGTCCACCTCTTTCTGGGGACACTGCATGACGGTCTTGTCACTGCTGTGGGGTTGGGGGCAGAGCCATGTGGGAAAAGGCATTTTGCATTTTGGCTATTACAGGCAACAATCATTTCTGTTCTCTGGGGTGTAGAATAGACAAGACTGTGTTTTATGTCTGTGTCGGGTGTGCGGAAATAATTTCCTGTTAAGGTTACCAAGTGGTAGAGCGGGAGGGCAGAGGTCACCCGATTGCAGCTGCCTCACTGCTGGGCTAACCACTGTTAACAGTTTGGCTTGTGTCCTTCCAGAGGTTTTCTATGCATTTACATAGATGCACAGAAATGAACCGTTTTAAAAACATGGTCGTCAGGTTTCATCACGAAGGCAGTGTGATGTGGTAGGAGTGGCCCTGGTCGGAACCAGGAGCCCTGGGACTGGTCCTTGCAGGACAGCCCCTGCCTCTTCCTTTTTTTCTGCTGGGGACTTGGGGCATCTGAGCTTGTTCTCGTGGTGGACGGGGTCCTCGTGCGTTTTAACCTCTCCTGTCAGCCTTTAATCTGCATTCCTTTGGGCCCCCGGAAATCGTGTTCTGTTCCTCCTGAGTAACCGCCGCTATCCGTGGTTTCTCGTAG
Seq C2 exon
GTTCGTGGGTAGATTCAAGTCTCGCAAAGAGCGGGAAGCGGAGCTTGGAGCCAAGGCCAAGGAATTCACCAATGTTTATATCAAAAACTTTGGAGAAGAGGTGGATGATGGGAATCTGAAAGAGCTCTTCAGCCAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000011257:ENSMUST00000080178:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(55.9=95.0)
A:
NA
C2:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGTCTGTGATGAGAACGGC
R:
AACTGGCTGAAGAGCTCTTTCA
Band lengths:
254-1378
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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