MmuINT0036108 @ mm9
Intron Retention
Gene
ENSMUSG00000056486 | Chn1
Description
chimerin (chimaerin) 1 [Source:MGI Symbol;Acc:MGI:1915674]
Coordinates
chr2:73462172-73463107:-
Coord C1 exon
chr2:73462934-73463107
Coord A exon
chr2:73462250-73462933
Coord C2 exon
chr2:73462172-73462249
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-Chn1:NM_175752:3
Average complexity
IR-C
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(37.7=33.9),PF0231811=FYVE_2=PD(45.3=72.9),PF087466=zf-RING-like=PD(48.7=32.2),PF0062022=RhoGAP=PU(9.1=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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: