MmuINT0115075 @ mm9
Intron Retention
Gene
ENSMUSG00000021223 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:MGI Symbol;Acc:MGI:2386139]
Coordinates
chr12:85123831-85124344:+
Coord C1 exon
chr12:85123831-85123968
Coord A exon
chr12:85123969-85124219
Coord C2 exon
chr12:85124220-85124344
Length
251 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGT
5' ss Score
9.73
3' ss Seq
TCTCTCCTCTCTCCACTCAGGTA
3' ss Score
12.08
Exon sequences
Seq C1 exon
GATCCGATTGGCAGGCTCGGAACCCTCCCTGGTACAGGCAGCTCCAGGGCAGGCGGTACAACTCTTTTGCCCTGGCAACATCCCCTCGGAATTCCAGGCAGGGTGGCAGAAAGAGGGCCGGCCCATCTCCTCTAACAG
Seq A exon
GTGCGTGTAAAACCATGGTCCCATCTCCTGCGTGAGAGATGCACTGTAAGATACTGGTGAGCAATCGCTACCTTCCACCTCTTGTATGTGCAATGTCCTCTCTTGTAGAGAAGCCCTTCTGGCATGCCTTAGAAATGTGAGAGGGCTCAGAGTGTTATGGGGCTATATGGTCTTCTCTGGTAGCATGGGAGCTGGAAGACTCTTACTGCCCTCAGGAGCCCAGAAATCACATCTCTCCTCTCTCCACTCAG
Seq C2 exon
GTACCAGCTCCAGGCAGATGGCTCCCTCATCATCAGCCGCTTGAGGCCGGAGGATGCTGGCATCTATAGCTGTGGCAGCCACAGGCCAGGCCATGAGCCCCAGGAGATACAGCTTCGAGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021223-Papln:NM_130887:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.979 A=NA C2=0.837
Domain overlap (PFAM):
C1:
PF0768612=V-set=PU(52.3=97.9)
A:
NA
C2:
PF0768612=V-set=PD(46.6=95.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATCCGATTGGCAGGCTCG
R:
TGTGACTCGAAGCTGTATCTCCT
Band lengths:
262-513
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: