MmuINT1026164 @ mm10
Intron Retention
Gene
ENSMUSG00000011257 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:MGI Symbol;Acc:MGI:2385206]
Coordinates
chr4:123292864-123294844:+
Coord C1 exon
chr4:123292864-123292959
Coord A exon
chr4:123292960-123294571
Coord C2 exon
chr4:123294572-123294844
Length
1612 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CGCGGCTGATCTTTTTTTAGGTG
3' ss Score
10.22
Exon sequences
Seq C1 exon
GGGGTGAATCTCTACATTAAGAACTTGGATGACACCATTGATGATGAGAAATTGAGGAGAGAGTTTTCTCCCTTTGGATCAATCACCAGCGCGAAG
Seq A exon
GTAAGAGCGTGTGCCAGCGTGGGTTTGGAAACAATTTTCTGTTGTTGGGTTAATGGTGTTAATTGTGTTGGTGGTCTAGAGAGTACCGTGTTCTAGCATATTCCTCATGCTCTGGAGAAGTAGGTTTGTAATATGCTATCTACTTGCACAACTGGAGCTTGGGCCAGTATCCCAATCCCCCAAGCGCCCTCTGCACTAAATCTTTCCCAGGCCTGCTGCCCGGTGCCGGTCTGGGGACAGACAGTGCTATACTACAGCAGAGGAAATCCAGACGGGTCGTTTCCATCCGCCCTGGGGCCTGTCTCTACAACTCTGCCACACTTCCTCTCTTGAGAATGAAGACTTTTTAAAGATTTAGTGGGCCTTTGACAGGAAAGTTTGGCTGGGCAGCCATGGTTCTGTGGGCATAGTCTACAGTAGGTCCTTGGCACTTAGGGGCTGTGACAGGCTGGTGTCTAGAAGTAGTGGGTTATGAGCTGACAGAATTCACTGATTGGTAGAGGCACACACGAGGCCTTTAGGTAGTAAGAAAGGCAGTTGGGTGGCGAGGGAGGGTTTGATGGTCTTCTGTGTAAGGTGTTGCCATTTGTATTGGTGTGGGCTTTTTGTTGGTTGTCTTTCATACAGGGTCTCACTTTTGTAGCCCTGACTATTTTAGAGCTCACCATGTAAACCAGGCTGGCCCAAAACTTGCCTGTCTCTGCCTCCTGGATGCTAGCAAGAAAGTGTGTGCCACCATGCCCTGCTATGGATGTTTTAAATGATCACTTTTGGAGTGCTGGCAAAAAGAACCCAGAACGGCTGTGGAGGTGACAGACAGCCCTGGCAAAAAAAACTTCTGGTTCCTCTTGCTGTCACCCACTTGACTGGCCCTGTTGGCATATTCCCCTGCAAAGCCCTATTAACAAAGTCCAGGTGACATTTTCAAGCCGATGGCAGGGCACTGTTCCATGGGTAAAAAACACTTAACCTGGTAACACACTGACCTTGGCGAGCTAAAGGGGCAGACATACAAGACACAGGAGAACAGTAAATAAGCCTTCAGTAAAGGGAAAGACGTTAAAGGCTGGCTCTGCAGAGGACCACAAGCACAGACCGCTGTGATATATTCAGGGTTGTCTAATAGAATGTGGGAACCAGGGCTGGAGAGATGGCTCAGTGGATAAGAGCACCCTACTGCTCTTCCGAAGGTCAGGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGAGATCTGACGCCCTCTTCTGGACAGCTACAGTGTACTTACATATAATAAATAAATAAATCTTAAAAAAAAAAAAAGAATGTGGGAACCAAGGCTCAGGGGGCTAGGAAGACTATAGTTATGATTAGAATAGGGTTTTCTGTCCTCCAGGTAACTGCCTCCCAATGACATCCCAGTCATTGACTTGGAAAAAAAGCTACAAACCTCTATTATTCATTTTTATGTGTGTTTTGTAGCTGGTCTAGAGTGGAGCCTCCTGCCTCGGCTCCCTGAGTGCTGACCTAGCCCAGTGGGCTTTTGTTGGCTTTTTGCTTCAGTTCTCAGTGCCTGTGCCTTCCTCACCACAAACCTCGCGGCTGATCTTTTTTTAG
Seq C2 exon
GTGATGCTAGAAGATGGGAGAAGCAAAGGGTTTGGCTTTGTCTGTTTCTCCTCTCCTGAAGAGGCGACCAAAGCTGTCACCGAGATGAATGGACGCATTGTGGGCTCCAAGCCTCTGTACGTCGCCCTGGCCCAGAGGAAGGAAGAGCGGAAGGCTCATCTGACCAACCAGTACATGCAGCGTGTGGCGGGGATGAGAGCACTCCCTGCCAGTGCCATCTTAAATCAGTTCCAGCCTGCAGCTGGTGGCTATTTTGTGCCTGCAGTTCCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000011257:ENSMUST00000080178:7
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=0.148
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(40.6=87.5)
A:
NA
C2:
PF0007617=RRM_1=PD(56.5=42.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAACTTGGATGACACCATTGA
R:
ACTGCAGGCACAAAATAGCCA
Band lengths:
343-1955
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