MmuINT0039424 @ mm10
Intron Retention
Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4530957-4531157:+
Coord C1 exon
chr6:4530957-4531010
Coord A exon
chr6:4531011-4531103
Coord C2 exon
chr6:4531104-4531157
Length
93 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TGTCTTTATCTCCCACCTAGGGT
3' ss Score
9.51
Exon sequences
Seq C1 exon
GGTGAAGCTGGTGCTGCCGGTCCTTCTGGCCCAGCTGGTCCTCGGGGTAGCCCT
Seq A exon
GTAAGTAGAAACCACAGCTTTTTGGATATTCATAGTTCATGGTTTACAGACATCTGAGAGGCTGTGAGTGTGATGTCTTTATCTCCCACCTAG
Seq C2 exon
GGTGAACGTGGTGAAGTTGGCCCTGCTGGCCCCAATGGATTTGCTGGTCCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029661:ENSMUST00000031668:35
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(4.1=16.7),PF0139113=Collagen=FE(19.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(19.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCTGCCGGTCCTTCTG
R:
AGGACCAGCAAATCCATTGGG
Band lengths:
95-188
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