MmuINT0039170 @ mm10
Intron Retention
Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:130076999-130077252:+
Coord C1 exon
chr4:130076999-130077052
Coord A exon
chr4:130077053-130077219
Coord C2 exon
chr4:130077220-130077252
Length
167 bp
Sequences
Splice sites
5' ss Seq
CTGGTGGGT
5' ss Score
6.29
3' ss Seq
TGTGTATCTGTCTCTCACAGGGA
3' ss Score
10.65
Exon sequences
Seq C1 exon
GGAGTGCCTGGACACAATGGTTTGCCAGGACAGCCCGGGCTCACTGCCGAGCTG
Seq A exon
GTGGGTATCAGCCAGGACACACTGGCCATCGTCCTTCCTGCCCTCCCTGGGAATGAGCTGGCCACTCAGCCCCGTTAGCTCTGGTGGGGGTCCTCCTTCTGCTCCTCTAGGCTGTGTAAACTTCCCCTCCCGGCCAGCTAGAAGCTGTGTGTATCTGTCTCTCACAG
Seq C2 exon
GGATCCTTACCCATCGAGAAACACCTCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690:ENSMUST00000044565:43
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.545
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(2.6=18.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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:
GAGTGCCTGGACACAATGGTT
R:
AGGAGGTGTTTCTCGATGGGT
Band lengths:
82-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types