MmuINT0039201 @ mm9
Intron Retention
Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:129732381-129732737:+
Coord C1 exon
chr4:129732381-129732434
Coord A exon
chr4:129732435-129732710
Coord C2 exon
chr4:129732711-129732737
Length
276 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
CCATGCCTCCTTTTTCTCAGGTC
3' ss Score
9
Exon sequences
Seq C1 exon
GTGGACGCGCAGCTCATGGGAAGAAACATCCAGAAAGCAGAAAGGGGGACAAAG
Seq A exon
GTAGAGATGGCGGCTGAGGGGGTGAGCCCACGGTGCCCTCTGTCTGCCCTGCATTCCCTCTATAAAACCCTTGGAAGAGATGCTGTACTCCCACTCTCTTCCTGCCCGGACAGAGCTTGGCTGCGCAGTGCCAGCTCTGAGAAGGGGAGACAGACTGGGCGGGACACAGTACTGGGCATTCTCTAGAGAGCTGGCTCCTGCCTGCGCTTGTACAGGGGCTTGGAGCAATGTTTGGTCCCAGGTTCCTCTCCCACTCCCATGCCTCCTTTTTCTCAG
Seq C2 exon
GTCCACCAGGGGACTGGAGTTAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690-Col16a1:NM_028266:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.950 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: