MmuINT0114447 @ mm9
Intron Retention
Gene
ENSMUSG00000054582 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:MGI Symbol;Acc:MGI:1922908]
Coordinates
chr2:163851186-163853404:+
Coord C1 exon
chr2:163851186-163851409
Coord A exon
chr2:163851410-163853210
Coord C2 exon
chr2:163853211-163853404
Length
1801 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
CTCCTTTGCTTCCCCTCCAGCGG
3' ss Score
9.25
Exon sequences
Seq C1 exon
TGCTGGCCCGCTTCTGGGTGCCCTGCGCATCATGGACACAGGTGGCCATGGCTGCTCACTCTCCTCGCTCTATGTGGGCGATCTGCACCCCGACGTGACTGAATCTATGCTCTATGAGATGTTCTCCCCGATCGGCAATATCCTTTCCATCCGCGTGTGTCGGGATGTGGCTACCCGGCGCTCTCTGGGCTATGCCTACATCAATTTCCAGCAGCCTGCTGACG
Seq A exon
GTGAGCTCTAGAGAAGAGAAAAACGCTTGCTTTTAACACTCTTGAGCCAAATACTTTCCTTTTGATAACTGCCATCCTGAACTGGAAAGCTTTCTTTCAAATGAACTTCTATTAGCTCAGCAATAGTGATTTTTCTATCTTTTAGGTGGAAATGGGCCTGTAGCTAATTGTGGGTATTTTACATTACAGATCATAGTCAGGGAAGATTGGGTAGCCTGTGTTTCCGTCTTCTGTATCATAGTTAGGGAAAATGAGGCCTGGAGACAGGGAGTTGGAAGGTAGGCATTCAGTCGCTGAGGGGAGAATTGGCAGTAACTGCTGGCCATGCTGGTTGTTGGTGAGTGGCTTTGGTATTAAGCAGAGCTGGGTTAGGAATCCAGGATCTGTGTGACAGCAGGCAAGTGGCTCAACCACTCTGAGCTCAGTTGGCTGTGTGGAAGGAAACTGGGGTTCTGCCTCCCTTGCAGAGTGGTTACATAGGAGATTGATAGCACCTGGGAGGAAGCTGCCCAAAGCCTTGCAGGTGGAGAGTGGGGAAGAGGCCGTGGGTTCCTGCCCTCCAGTGTAGCCTGACGTGAGGGCTACCCCAGGTGCCTCACCTCTCTGATTCTGGAAGAGCCGCCTCCTGTAGGCATTGCCAGCCACTGGCAGGGTGAAAGCATTGATTAGTAATTGTCAGCCGAGCACGTCTGGTCTTCCGCTGAAAACAGAGGACAAAGGTTAAGAACCATGGTTTTGCTGAGGCTGTGCCACCGGGCAGGACCACCCTTGGTGAGAGGCCAAGGCTCGTTTCTCTGGGTCATGAAGAATGGGGATCCCGAGTGTGAAGTACCATTAGGGACACTGGATGTATTCTCAAGTGCAGTGTAAGAAAACCACTCCAGAGATGTAACCAAGAATTGTCCTTCCCCACCTACTGGGAAAACCCTGGCAAGAACATGAATTTGAGGCCAGCCTGGGCTACATATTGAGATCCTATCTCAAGATGAAGTAGTTCAGGCCTCCTGTGTGAGTTAGGAGTTTCCCTGAAGCCAGGATGTTCTTGCCCTCCGCTACACTCCACGTCTGCCTATGCCTGTCTGCAAAGCTCCTGACTGAAACAGAGTCTGGCCATCAGGGCCCGGTCCATAGATGGGAGATCTGAACTTTGGAGATCCTGACTGGGTGTGTTAGCAATGGATGAAAAATGCAGGCTTCTGTGGCCTGCGCCACTGCATTCCGTTTGCCTCTTCTGTGCCTCTGAAGCGAGCAGGGTCCTTGAAGCAGGCAGCACATTATCTGCAGGGAATAGGCTGTCCAAGTAGAAGGGTGCTGAGCAGAGATGTCCAGTTGTGCATATGCCGCCATTTATCAAACATCTTTTCCCTGCGTCACACAGAAACCAAGTATCGTTCATTGCACGTTTTACATAGCAACCTGTTTGACAGCCCGGCAGTAGGGGATGTTCATTTAGGTGTAGGAAGGAAGGTGCCGTCACCATCTCCTCACTTCATGGGTGGGGATGAGGGACGGGTCATGGGGGTTCACTTTCCTTTCCTCTTTGCATGCTCACCCACGAAATGTGTGTCCAAGGCCGGGAGAGCCCGGCTCTGCCTTTGCAAGCTTCAGCCTCTCCACGTGTGTGATGGGGAATCCATGCTATTTACTGAGAGTTGCTCTTTCTGCAGTGTGTGAGGAGTACGTGGACAATCCCCTCAGCGGAATCCACCAGTGACCCAGGCCGTGGCTTTCCTTTCCTCTATCCTAGAAGGACACAAATGTCACCTAACTTGCCCCTTTCTCTCCTTTGCTTCCCCTCCAG
Seq C2 exon
CGGAACGGGCACTAGACACAATGAACTTTGAGGTGATCAAAGGCCAGCCCATCCGAATCATGTGGTCCCACCGAGACCCAGGCCTTCGGAAGTCTGGTATGGGCAACATCTTTATCAAAAACTTGGAGAATTCCATCGACAACAAGGCTCTGTATGACACCTTCTCTACTTTTGGGAGCATTCTCTCTTCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054582-Pabpc1l:NM_001114079:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(73.2=80.0)
A:
NA
C2:
PF0007617=RRM_1=PD(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCATCATGGACACAGGTGG
R:
ACAGAGCCTTGTTGTCGATGG
Band lengths:
352-2153
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: