MmuINT0039498 @ mm10
Intron Retention
Gene
ENSMUSG00000079022 | Col22a1
Description
collagen, type XXII, alpha 1 [Source:MGI Symbol;Acc:MGI:1916950]
Coordinates
chr15:71915106-71915837:-
Coord C1 exon
chr15:71915784-71915837
Coord A exon
chr15:71915160-71915783
Coord C2 exon
chr15:71915106-71915159
Length
624 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGA
5' ss Score
10.1
3' ss Seq
TTTTAAACTTCTTCTTTCAGGGT
3' ss Score
10.78
Exon sequences
Seq C1 exon
GGCCCGCCTGGACCACCCGGTGTTCCAGGGCCCCCTGGACCTGGAGGACCCCCG
Seq A exon
GTAAGACTGGCTTGACTTTCTCTTGAAGGGGAACTTGGGTAGCATTTTCAAGGGAAGGGGTGGCTTTGTCCTGTATCCAGAACAAAGGCGCAGACAGGAAGACTGTGGATGTAGAAGCCTCCATGCTTCGTCACTCTTAAGCTCTTGGGTCTGGCACTTATAAGTGACATATAAATCATCGTAAACACTTGGTATCTTCTTCTGTCATGGTATGGGGGTGCATCAGGTTGGCCTGCTATCCAAGTATGCATAGATTTTTGTGGTCAGTTCTCACAAAACAATACCAAGGCCAGTGTTTGTTTAACAGTCTTCCCTCTCATCCTTTAAAGATCAGCTGGGAAACTGTCCCATAGCAGGTGGTGGGCAGGGTACACCCAGCAGTCTGCAGAGGGAGTATTCGGGCTTGGGTGCACATGGCAGTGGTCTCGGCTGCAGAGCAGACATGCTGCAACCTCACCAACTGTAGATCTGGGGCTATTCTGTGTTTTACAGGGGCTGGCAATGAGAGTGGTAGACACCCTGAGGCATTCTCCTTAGAGCCAGAGGCCTGATCCTATGCCAGGGACGGCATCATGACAAGACTAATCTCAAATAGACTGACAGTTTTTAAACTTCTTCTTTCAG
Seq C2 exon
GGTTTACCTGGCGAGCTCGGCTTCCCGGGAAAACCTGGGCCTGCTGGGCATGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079022:ENSMUST00000159993:24
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(20.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.9=100),PF0139113=Collagen=PU(11.0=44.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
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
- 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