MmuINT0039199 @ mm10
Intron Retention
Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:130054146-130054474:+
Coord C1 exon
chr4:130054146-130054226
Coord A exon
chr4:130054227-130054348
Coord C2 exon
chr4:130054349-130054474
Length
122 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
ACCTTTCTCCCACATTGCAGTGT
3' ss Score
8.59
Exon sequences
Seq C1 exon
TTTGACCTTCAGCAGGCGCACATCTACTGCGACCCGGAGCTGGTGCTGGAGGAAGGCTGCTGTGAGATCTTACCGGGAGGG
Seq A exon
GTGAGTAGTTGGCTCCTAGCACATGCTGCGCTGGAGAGGGGGCAGCCTGCACAGGGACGGCAGAGGTCTGAGGATGCATCTGCCTCTGTGCTGACCCTGGCTACCTTTCTCCCACATTGCAG
Seq C2 exon
TGTCCCCCAGAGACCTCCAAGTCACGCCGGGACACCCAGAGCAATGAGCTCATTGAGATCAATCCTCAGACAGAGGGCAAGGTCTACACCCGGTGCTTCTGCTTGGAGGAACCTCAGAACAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690:ENSMUST00000044565:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.429
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=PD(2.7=11.1)
A:
NA
C2:
NO
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:
CCTTCAGCAGGCGCACATCTA
R:
CTTGCTGTTCTGAGGTTCCTCC
Band lengths:
202-324
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