MmuINT0039450 @ mm9
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180733290-180733959:+
Coord C1 exon
chr2:180733290-180733413
Coord A exon
chr2:180733414-180733822
Coord C2 exon
chr2:180733823-180733959
Length
409 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
GGCCTCGTTGTGCCTTACAGCTG
3' ss Score
8.35
Exon sequences
Seq C1 exon
GTACATGTGGGACAGCCTGAGGTACTGCTGGATGGTCTGGAGCCTGGCCAGGACTATGATGTCTCAGTGCAGAGCCTTCGGGGACCAGAGGCCAGCGAGGTCCAGAGCATCCGTGCCAGGACCT
Seq A exon
GTGAGTATCTGGTCACACAGCCCAGCGTTCTCAACCTTCCTAATGCTGTGACCCTTTAACACAGTTTCTCATATTGAGGTGACCCCCCAACCATAAAATTATTTTTTGTCACTACCCCATAACTGTGATTTTGCTACTGTTAGGAATTATTATGTAAATATCTGTGGTTTGGATGGCTTTAGGTGACCCCTATGAAAGGGGGGAGTCATTCAATTCCCAAGGGGTTTGGGACCCACAGGTTGAGAACCTCTGACATAGCAGTTCCCCAGTTCTGTTGTTTACTTTGCTCTAAGTGGGAGACCACAGATAACCCTGGATGACCCATATGCCCTCAGGCCCAGTACCTCCCACTCTTCTCTCAGTCCCAAGGGTAGGGTGCCAGCCCCTGAGGCCTCGTTGTGCCTTACAG
Seq C2 exon
CTGCCCTGGGGCCCCCAAGACACCTGACTTTCTCAGATGTTCGCTACAACTCAACCTGTGTGTCCTGGGAAGCCCAGAGGCCTGTGCGCCTGGTCAAGGTCAGCTACATCTCTAGTGATGGCAGCCACTCTGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-Col20a1:NM_028518:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.743 A=NA C2=0.113
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(40.5=76.2)
A:
NA
C2:
PF0004116=fn3=PU(53.8=91.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACATGTGGGACAGCCTGAGG
R:
AGAGTGGCTGCCATCACTAGA
Band lengths:
254-663
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: