MmuINT0039480 @ mm9
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180731060-180731556:+
Coord C1 exon
chr2:180731060-180731212
Coord A exon
chr2:180731213-180731386
Coord C2 exon
chr2:180731387-180731556
Length
174 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CTGATTGCCTTTCCTCACAGTCA
3' ss Score
8.7
Exon sequences
Seq C1 exon
GTGTGAAGAATGTCGATGAGGCTGAGCTGAAGCTCCTGGCGTCCCAGCCACTGGACATCACTGTCCACAACGTGCTGGACTTCCCTCAGCTGGACACCCTAGCTCCTCTGCTCAGCCGACTCATTTGCCAAAAAATTCAGGGCAGAGGCCCAG
Seq A exon
GTAAGAACACAGCACCACGGTGGCAGAGGAACAGGGAGATTGAAGCTATACTGGGCCAATTCCTTGGATATGTTGTGGGCTGGGGTAGGAGGATTTTCCTGTCCTTCCTGTACATGGCCACCAGAGGGAGTATGTGGATGTGCTTGCTTGGTCCCTGATTGCCTTTCCTCACAG
Seq C2 exon
TCAAACCAGCAGCAGGTACTCGGGTCCTGGACCCCCTCCCCACGCCCACCAGACTGATCCTGACCCACGCCACCTCATCCAGTATCCACCTGTCTTGGACTCCAGCCTTATACCCACCCCTCAAGTATCTAATTGTATGGCAGCCTTCTAGGGGTGGTGCCCCCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-Col20a1:NM_028518:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.070
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=71.2),PF0385310=YjeF_N=PD(41.0=78.8)
A:
NA
C2:
PF0004116=fn3=PU(53.8=75.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCGATGAGGCTGAGCTGAAG
R:
CTGGAGTCCAAGACAGGTGGA
Band lengths:
247-421
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: