MmuINT0036108 @ mm10
Intron Retention
Gene
ENSMUSG00000056486 | Chn1
Description
chimerin 1 [Source:MGI Symbol;Acc:MGI:1915674]
Coordinates
chr2:73624115-73625050:-
Coord C1 exon
chr2:73624877-73625050
Coord A exon
chr2:73624193-73624876
Coord C2 exon
chr2:73624115-73624192
Length
684 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CATTCATTCATTTTTTTCAGGTC
3' ss Score
11.18
Exon sequences
Seq C1 exon
ATTGTGGGTTGAATGTTCACAAGCAGTGTTCCAAGATGGTCCCCAATGACTGTAAGCCAGATCTGAAGCACGTGAAGAAGGTGTACAGCTGTGACCTGACAACGCTCGTGAAAGCTCACATCACCAAGCGGCCAATGGTGGTAGACATGTGCATCAGGGAGATCGAGTCCAGAG
Seq A exon
GTGAGGTGTTTGGACGAAGGCTGCCGACGCCTTCACTTGGGGCTCCCTAGGCGCTTGCCTTGTCATTGATGTGGGGAATGGTGTCAGGAGACGTGTGCTCTCACAGTGCAGTGTATTAATGAGCAAGCAGCTTGATTTCAAGGAACATTTAACTGGTGATGGAAAGTAGTATTTAGGATACATTAATGGATGGTGTCTGCAGTCTGCAAAAATCTCTGGGCAGAGATGTATTCACCTTTCAGGTTTTAAGTTCTTCTCATGCCAGGACAAAGACAGAAATGCCCTATTAAAACGTCCAGAGCAGAAACCTGAGCCGCACCCTAATTATTCTTGCCCCCTTGGGAAAACAGCCATAGGCCTGCTGATGCAGGCTTTCTGTTCTGTAAAAGACTTTATGATGGAATTGGGTGATGAATGGTCTCCCTTAAGATTTAACATTACTTGGTCTAATTAGGCAACATGATGGCCAAATTATAAATATCCAGGTGACAGTAGGTCAGAAGTAAAAATTGTGGAACAGATTCACTTTTGGAGGATGTGGGAGAAGACTTCTAGGCATGTGTGTTTTTTCTAACACATCGTTTGTCCAGCTTGAAGTATGGAGAGATGTTGAAATGAGAAGGAAAGTCATGAGTTAACAGAAAAGTAGTTCCCATGCTTCATTCATTCATTCATTTTTTTCAG
Seq C2 exon
GTCTTAATTCTGAAGGACTCTACCGAGTGTCAGGATTTAGTGACCTGATTGAAGATGTCAAGATGGCTTTTGATAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056486:ENSMUST00000112024:9
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=0.000
Domain overlap (PFAM):
C1:
PF0013017=C1_1=PD(60.6=33.9),PF087466=zf-RING-like=PD(73.8=52.5),PF0062022=RhoGAP=PU(56.0=23.7)
A:
NA
C2:
PF0013017=C1_1=PD(0.1=0.0),PF0062022=RhoGAP=FE(17.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGTGGGTTGAATGTTCACAAGC
R:
TCAAAAGCCATCTTGACATCTTCA
Band lengths:
246-930
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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