MmuINT0039009 @ mm9
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61356663-61356808:-
Coord C1 exon
chr10:61356782-61356808
Coord A exon
chr10:61356690-61356781
Coord C2 exon
chr10:61356663-61356689
Length
92 bp
Sequences
Splice sites
5' ss Seq
CCGGTTTGT
5' ss Score
4.86
3' ss Seq
TCATTTCCTTCTCTTTGTAGGGA
3' ss Score
11.34
Exon sequences
Seq C1 exon
GGCCTGGTGGGTCCTCGAGGACAACCG
Seq A exon
GTTTGTAACTCCCTTCCTTGTCCCCAGCAGGGAGGTTGGGGACCATGTGGCCTGGAATTTGAGCCCTGACAGTCATTTCCTTCTCTTTGTAG
Seq C2 exon
GGACCTCAGGGACAAAAGGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806-Col13a1:NM_007731:11
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=FE(12.9=100),PF0139113=Collagen=PU(9.1=88.9)
A:
NA
C2:
PF0139113=Collagen=FE(12.9=100),PF0139113=Collagen=FE(9.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGTGGGTCCTCGAGG
R:
TCTCCCTTTTGTCCCTGAGGT
Band lengths:
48-140
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: