MmuINT1026148 @ mm10
Intron Retention
Gene
ENSMUSG00000022283 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]
Coordinates
chr15:36601315-36602985:-
Coord C1 exon
chr15:36602846-36602985
Coord A exon
chr15:36601410-36602845
Coord C2 exon
chr15:36601315-36601409
Length
1436 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATG
5' ss Score
4.83
3' ss Seq
CTCTGAATTACTTTTTTTAGGGC
3' ss Score
7.7
Exon sequences
Seq C1 exon
GTTTGTTGGACGATTTAAATCTCGGAAGGAACGAGAAGCAGAGCTTGGAGCCAGGGCAAAGGAGTTCACCAATGTTTACATCAAGAACTTTGGAGAAGACATGGATGATGAGCGCCTTAAGGAACTCTTTGGCAAGTTTG
Seq A exon
GTAATGTGTCAAAGTTAAATCTTTATACTTAGAGTAATTGTCTAAAGTTAATGACTAATATTTGACTAGTAAGTTTTAACACTTGATTTGAATTAGGCTATAGTTCACTGCACAAGAGTAATATGCAAGTGGAATGCTGTACAGTGACCAACACGAGCCGTGGGTGGCTGAGGAGATGTAAAGGGTTTGCCACATTAAGTAAGATCCTCTGAGTGCAGACATTAGTGTGAGGTAGGTGGGTGATGTCGGGATCCTGGAGTAAAAGACGAGGAAGGCAGGATTATTTGTAGGTGACTTCCTCCCTTTCTGTTGAGCCTAGGAATGGCCTTTTTTGTTTGTTTATCTAGTTCTGTATTATATCTAACATCATAAAGCTGTGTTGAGCTTTGACAAAGACAGGACCTCAGAGTTGCAGCTCTGGCAGGCACACAACTCCCAAGAGATGCCTCCTGAGTCCTGGAATTAAAGGCACAAAGCACCACACAGGGCTGAATCCTCTTTTAAGCAAAAGGAATTGTGATTCTTCACAAGTACCAATCATGTAAGATGACAGTCATGTTTTTTGCACCTCATTCAGTCAAGTTTCTCTTGTATATCATTTGTCTTGCACCTGGGAGTTTTAAAATAAAAAAACATTTTTTGGTGGTATGGGGTGGGTCTCTGGCCTTGGACTTACTATGTATATACAAGGTTGGACTTGGAGAGATCCACTAGCTGCCTCCCAAAGGCAGATTGGATTATTTTTATTTAATTTAATTTATTTTATTTTTTAAAAAAACCTTACACCACCTCTTGTACAGCCTGGCTATAGACCACTGTCTTTTCTTTTGCTAAGTGCTAAGACATTACGGCTAAGGGGGCTTACAGTCTAAGGTGTATCCATGACCGTCATGGCAGGGGATATGGTGGCAGGTAGGCATGACAGTGGAACAGCAGCTGAGAGCTTACTTGTTACAACAACCACAAAGCATTTTATGGTATGGGTCTTTGGAAACCTCAAAGCCCACCAATCAACTGAGGACCAAGTATTGAGATGTATGGGGGCCATCATTCAATCACTCCTAGTTCTTTCTGTGCCTGAGCCTGCTTATGGTCTCCACAAAAGGGGAAGGCAGAACTTGTGTTTTAAGAAACATTCTTTCAGGTATTTTATGCCTGCAGATCTAGCCATTCTCTGTACTTACTGTTGAAAAACAGAAGGCTTTGAAGGATTATTTTGAACAAGAAAAATCAAGTTAATGATGTAAAGGGACAACTACTGAGCTAAGAATAAAATCTTCCATAAGCTTGAAAGAAATCAAACAGTATTTAGAAGTGCATATGGTAGACCAGTAAAACCTTAGGGCTGGGAGGGCTGGGACTTTTGTGTTACATGTTAGGACATGAAATGTGTACATTAAGTGGACTACTGAATTACTCTGAATTACTTTTTTTAG
Seq C2 exon
GGCCTGCCTTAAGTGTGAAAGTAATGACAGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGGCATGAAGATGCGCAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022283:ENSMUST00000001809:4
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(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
A:
NA
C2:
PF0007617=RRM_1=FE(44.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGGACGATTTAAATCTCGGAAGGA
R:
CATCTTCATGCCTTTCAAAGCT
Band lengths:
222-1658
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