MmuINT0039898 @ mm9
Intron Retention
Gene
ENSMUSG00000031502 | Col4a1
Description
collagen, type IV, alpha 1 [Source:MGI Symbol;Acc:MGI:88454]
Coordinates
chr8:11219987-11220376:-
Coord C1 exon
chr8:11220209-11220376
Coord A exon
chr8:11220077-11220208
Coord C2 exon
chr8:11219987-11220076
Length
132 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
AACATTTCTTTTGACCATAGGTT
3' ss Score
8.27
Exon sequences
Seq C1 exon
GTCCACCTGGAATTAAAGGAGAGAAAGGGTTCCCTGGATTCCCCGGACTGGATATGCCTGGCCCCAAAGGCGATAAAGGCTCTCAAGGACTTCCTGGCCTCACAGGACAGTCAGGCCTCCCTGGCCTTCCTGGACAGCAGGGGACACCTGGAGTTCCAGGGTTCCCAG
Seq A exon
GTAAGTGACACCTGAACTTGGCCTGGATCACTCAAGAGGGAGCATGGCTTTCTTCTTTCCTGAATCCAGGCCATTTACCTACCACTGGAGGTCCATGTGGGGATGTGTTCTTAACATTTCTTTTGACCATAG
Seq C2 exon
GTTCTAAAGGTGAAATGGGTGTCATGGGAACCCCGGGACAACCAGGCTCGCCAGGACCAGCAGGCACCCCAGGGTTACCTGGAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031502-Col4a1:NM_009931:32
Average complexity
IR-S
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(31.1=33.3),PF0139113=Collagen=PU(65.0=68.4)
A:
NA
C2:
PF0139113=Collagen=PD(33.3=64.5),PF0139113=Collagen=PU(40.7=77.4)
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:
TCCACCTGGAATTAAAGGAGAGA
R:
GGTGCCTGCTGGTCCTGG
Band lengths:
235-367
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: