MmuINT0039960 @ mm9
Intron Retention
Gene
ENSMUSG00000031503 | Col4a2
Description
collagen, type IV, alpha 2 [Source:MGI Symbol;Acc:MGI:88455]
Coordinates
chr8:11443071-11443415:+
Coord C1 exon
chr8:11443071-11443232
Coord A exon
chr8:11443233-11443316
Coord C2 exon
chr8:11443317-11443415
Length
84 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
CTGTCCTGTCTTCATTGCAGGGC
3' ss Score
11.06
Exon sequences
Seq C1 exon
GCTACCAAGGCCCTCCAGGACCACCTGGGCCAAACGCACTTCCTGGAATCAAAGGAGATGAGGGGAGCTCTGGAGCTGCAGGATTCCCTGGACAGAAAGGATGGGTTGGGGACCCAGGGCCCCAGGGCCAGCCTGGTGTACTCGGTCTTCCGGGGGAGAAAG
Seq A exon
GTACAGTGTGGGGCCGGTGCTGTGGGCAGAGGGCTGCAGAACCAACATGGTGCCCTGGTCTTAACTGTCCTGTCTTCATTGCAG
Seq C2 exon
GGCCCAAGGGTGAACAAGGATTCATGGGCAACACCGGGCCCTCTGGGGCCGTGGGTGACAGAGGCCCCAAAGGACCCAAAGGCGACCAAGGATTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031503-Col4a2:NM_009932:42
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(74.3=94.5),PF0139113=Collagen=PU(19.0=21.8)
A:
NA
C2:
PF0139113=Collagen=FE(52.4=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:
ACAGAAAGGATGGGTTGGGGA
R:
GGAATCCTTGGTCGCCTTTGG
Band lengths:
167-251
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: