MmuINT0039019 @ mm9
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61336742-61337518:-
Coord C1 exon
chr10:61337486-61337518
Coord A exon
chr10:61336769-61337485
Coord C2 exon
chr10:61336742-61336768
Length
717 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
CCGCCTTCTTTCCCACACAGGGT
3' ss Score
10.15
Exon sequences
Seq C1 exon
GGGGTTCCTGGGATTGCCGTGGCTGGGATGAAG
Seq A exon
GTAGGTAAACCCTGTCACTGTGTCAAGATACCACAAAGCAGGGGTTCGGGCTCAGCAGCATCGTAGCTGGATCCAGGAGAGGTCAGATGTTTCAGCCAGGTCTCCAGACTCCACTCAGGGTCTCTTTAGTCTGCCACTGAGAGAAGCCAGCTCTGTCCCATACTCCAGAGCGAGCCGCCGTGGGCTTCCAAAGACTCTAAGAGCCAGCATCTTTTCCCTGAACCCCTTACCAAGGCAGGGGTTGTATCCTGGCAAGACAGATTCCCAGTGTTGATCTTTTAGCAGCTCTTCCCACCAGGAGGACCACCCCTGAGATGCTCCAAACCTTCCCATCCTTTGAGGGCAGTGTTTCTCAACTTGTGAGTTGTGACCCCCCTTGGGGGGGAAGGGTCAAGCAACCCTTTCACAGGGGTTGCCTGAGAGCCTCAGAAAACACAGATATTTACATTACAACTCATCACACTAGCAAAACTGCAGTTATGAAGTAGCAATGAAACTCATTTTACAGTTGGGGAGTTGGTCCAACATGCAGAACTGTATTAAAAGATCGTGACATTAGGAAGGTTGGAAACCACTGGTCTGGAGGGGAGGGGATGAGACCCTCCAGAGCCTCTGCCCTGGGGTGTCCCCTAAGCAGAGGAAGTGGCCCTCCTGGAAAGCAGAGGGCCCTTGGTTCTGCTTTGTCTTTTCTTCACTGCCGCCTTCTTTCCCACACAG
Seq C2 exon
GGTGAGCCAGGGACGCCAGGAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806-Col13a1:NM_007731:20
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(10.9=54.5),PF0139113=Collagen=FE(15.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(12.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: