MmuINT0039461 @ mm9
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180741831-180742430:+
Coord C1 exon
chr2:180741831-180741940
Coord A exon
chr2:180741941-180742271
Coord C2 exon
chr2:180742272-180742430
Length
331 bp
Sequences
Splice sites
5' ss Seq
AAGGTCCTG
5' ss Score
-0.19
3' ss Seq
ACTTACTGTGGTTTCTGCAGGTA
3' ss Score
10.34
Exon sequences
Seq C1 exon
CTGGCAGAAAGTCTCTGACTTACTTCAACCATGATTCCCGGGCAGCCTTGCAGGAGGTCACCTTTGACCTGCAGGATGCAAAGAAGATCTTCTTTGGAAGCTTCCACAAG
Seq A exon
GTCCTGGGAACTGTCTGTCTGAGCCCTGACCCTCTGGCCTGTCCCTCCCTGCATGTGGTTGTCTTCTGTGAGAGTCAAACACTGATTTATATAGAGCCTTTGACCCTTGTGCTCCGCTGTTCTGACTGTCCCTCCTTAATTTGGGTCAGAGAGCAAACTCTTTTTTGGGGGGGCGGGGAGGGGGGAGGCTCCTTCAGCAGCTTTCTCTGAGAAGCCAAGGCCTCAGTAGGTTCCAGAGTAGAGTCAGAATTTGATCCCAGACCCTATGTGTTGGCCCCTTTAATCTGTCTTGATGTGATCTGGGGTGCGAGACTTACTGTGGTTTCTGCAG
Seq C2 exon
GTACATATAGCTGTAGGCCACTCTAAGGTCAGACTCTATGTGGACTGTCGGAAGGTGGCCGAGCGTCCCATTGGGGATGCTGGCAGCCCACCCACAGGTGGTTTCATCACACTAGGGAGGCTAGCCAAGGCCAGAGGGCCACGGAGCAGCTCAGCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-Col20a1:NM_028518:22
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=0.338
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TGACTTACTTCAACCATGATTCCCG
R:
TGTGGCTGAGCTGCTCCG
Band lengths:
254-585
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: