MmuINT0114454 @ mm9
Intron Retention
Gene
ENSMUSG00000054582 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:MGI Symbol;Acc:MGI:1922908]
Coordinates
chr2:163857916-163858318:+
Coord C1 exon
chr2:163857916-163858055
Coord A exon
chr2:163858056-163858223
Coord C2 exon
chr2:163858224-163858318
Length
168 bp
Sequences
Splice sites
5' ss Seq
TTGGTGGGC
5' ss Score
3.03
3' ss Seq
ACCTGTTTGGTCCTTCCTAGGAA
3' ss Score
9.98
Exon sequences
Seq C1 exon
CTTTGTAGGCCATTTCAAGTCTCGACAGAAGCGGGAGGCAGAGCTGGGGGCTCGGGCCCTCGGGTTCACCAACATCTATGTGAAGAACCTGCACGCGAACGTGGACGAGCAGAGGCTCCAGGACCTCTTCTCCCAGTTTG
Seq A exon
GTGGGCATGCTCCCCAAAGGAGGAGGGGGAACACTACTGCTCTTCTTCCATGCCCAGGTCAGGTGGGAGGAGGGCTTCTTCTGGGATTCCTGGGGACTTATAGAAGAAGGAAGAGACCATGCAGGCCCCTCCCCCGACTCCCTGCTAAACCTGTTTGGTCCTTCCTAG
Seq C2 exon
GAAATATGCAGAGTGTGAAGGTGATGAGAGACAGCAATGGGCAATCCCGGGGCTTCGGCTTTGTCAACTTTGAGAAGCATGAGGAAGCCCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054582-Pabpc1l:NM_001114079:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.062
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
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGTAGGCCATTTCAAGTCTCGA
R:
CTTCTGGGCTTCCTCATGCTT
Band lengths:
234-402
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: