MmuINT1026158 @ mm10
Intron Retention
Gene
ENSMUSG00000011257 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:MGI Symbol;Acc:MGI:2385206]
Coordinates
chr4:123297861-123298832:+
Coord C1 exon
chr4:123297861-123298093
Coord A exon
chr4:123298094-123298512
Coord C2 exon
chr4:123298513-123298832
Length
419 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
TTGGCACTTCTCTTTTCTAGGAG
3' ss Score
9.31
Exon sequences
Seq C1 exon
GGGAGCGTCTGTTCCCGCTTATCCAAACAATGCATTCAAACCTGGCTGGGAAAATCACCGGGATGCTGCTGGAAATCGACAACTCTGAGCTGCTGCACATGCTGGAGTCCCCCGAGTCCCTCCGCTCCAAGGTAGATGAAGCGGTGGCAGTCCTGCAGGCTCACCATGCCAAGAAAGAAGCTGCCCAGAAGGTGGGCACTGTTGCTGCTGCTACCTCTTAGACAAGAAAAAAA
Seq A exon
GTATGTTGACAGTTCGTGTTTTCTGCCCCCTTTGGTTTTTCAGATAGGGCCTTACCATATGTTCCAGGCTGTTGGGGGTGAGGGGGTATATATATAATAAAACAGGATCTGCAATCCCAGCTGCCCATGTGGGCCAGGGACCTTTCTAGCTTGGCCTGAGGTTGTGTCCACTGCCTAGCTGTGAGTGCAGTGTGCAGAGAGGGGTGTTGGTATTTATTACAGTCTTGTTGAAGAGATCACTGTAGTGATGTCTGAGCTGTGGCCCCTGCAAGGTTTAGGAGAGAGTGAACTGGGACTCTTGATAGGGGAAAGGAGAAGGCGATGAGTTGCAGCCGGCTGGGAGCAGCTGGTGCTGACGAGCAGAGAGGTCTCTTTAACAAACAGGCTTGCTTATTTGTGTTGGCACTTCTCTTTTCTAG
Seq C2 exon
GAGTCGAAAGCCAAATAACCCCTCATGGCATCCAGCTAAGGTCTGAAGACATCCTAGTTTGTCTGTGGACCTCCACACCAAGAACCAAGTTGCAAATTCAATAGGTCATTTTGTATCAGAAGGTCAATTATGAAGCACCTATAAGTTTTTCAATTATAAGAATATATTCTCTGGGTTCTGTTGTGACCCAGATGATAACTTTTTTTTTTCTATTATGGGTTCTGGTTTTTTTTTTCCCTCATCCCAGAAATTGGTTTTGATGTACCCAAGACTTAAGTTTCTCAAATAAAGGAAATAAAATCTCCATAAATATGGCTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000011257:ENSMUST00000080178:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.356 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0065813=PABP=PD(70.8=68.9)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACTCTGAGCTGCTGCACATG
R:
CTGGGTCACAACAGAACCCAG
Band lengths:
344-763
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