MmuINT0039792 @ mm9
Intron Retention
Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97829285-97829722:-
Coord C1 exon
chr15:97829706-97829722
Coord A exon
chr15:97829318-97829705
Coord C2 exon
chr15:97829285-97829317
Length
388 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
GTCGATGTTTTGTGATGCAGGGG
3' ss Score
5.53
Exon sequences
Seq C1 exon
GAAAATTAGGGCCAAAG
Seq A exon
GTAAGGCACCCCATTTTTAATTTAATTTAATTAATCTAATTACATTCTCACTCCCTGCCCACGCGATTGTATGTATGAGCGTGGACACAAGCGTGCTATGGCGCATGTGTGGCGGCCCGAGGATAACATTGAAGACTTGGGTCTCTCTTCCCACCATAGGGCATTAGGGCGGCTCTGTCAGAGCCTTAGCCACCGGGCCATTTCACTGGTCCATGTTTTGCTTTCATGTGTCGTGTCCTTCTTCAGGGGTACTGAGATACTAATCTGGTCTGTGCCTCTTCTTTAGCCCTCAGATGTCCATCTGAGAGGCTAGGGTTGTGGGGTGGGGTTCTGTGTGGGGGCTCAGCGGGCTTGCTCAGCCTTCACCTGTCGATGTTTTGTGATGCAG
Seq C2 exon
GGGCAGAAAGGAGAACCTGGAGATATCAGAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483-Col2a1:NM_031163:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.767 A=NA C2=0.821
Domain overlap (PFAM):
C1:
PF148281=Amnionless=PD(2.7=33.3),PF0139113=Collagen=FE(11.4=100)
A:
NA
C2:
PF148281=Amnionless=PD(3.5=25.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: