MmuINT0039775 @ mm10
Intron Retention
Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97994544-97994921:-
Coord C1 exon
chr15:97994868-97994921
Coord A exon
chr15:97994589-97994867
Coord C2 exon
chr15:97994544-97994588
Length
279 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
CTATATGTCTCTTTCTCCAGGGT
3' ss Score
10.13
Exon sequences
Seq C1 exon
GGTTACCCAGGCCTCGACGGTGCTAAGGGGGAAGCTGGTGCTCCGGGTGTGAAG
Seq A exon
GTAAAGGGGCCACAAGACACACAGGGGGTGGCGGTAGGGGACAACTGTCCAGTCAAGGCGGCGCTGATGGGGTCGGGAGTTAGAACATAGCTGGGAACACCCAGTCTACATCTTGGTACATGAGCAGCAGGCCTTAGAGTTTGGGGACATCGTCTCTCCCCGGACTGAAATTGACATGTCTCAGGCCTAATTGAGCCAGCCAGACCTATCGATGACTTACCTAGGAAGTTTCTGGAAGCCAAGACTCCAGACACTGACCCTATATGTCTCTTTCTCCAG
Seq C2 exon
GGTGAGAGTGGTTCCCCTGGTGAGAACGGATCCCCGGGCCCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483:ENSMUST00000023123:14
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=FE(28.3=100),PF0139113=Collagen=PU(13.6=61.1)
A:
NA
C2:
PF0139113=Collagen=PD(13.3=53.3),PF0139113=Collagen=PU(16.7=73.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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
- 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