MmuINT0039477 @ mm9
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180728905-180729701:+
Coord C1 exon
chr2:180728905-180729063
Coord A exon
chr2:180729064-180729581
Coord C2 exon
chr2:180729582-180729701
Length
518 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGT
5' ss Score
7.92
3' ss Seq
CAACCAAAGCCCACCCCTAGGTC
3' ss Score
1.74
Exon sequences
Seq C1 exon
ATCACCCCCAGTTCCAATGTACACCCCCAACACCTGCTGATATAATCTTCCTGGTGGACGGGTCCTGGAGCATCGGCCACAACCACTTCCAGCAGGTGAAAGACTTCCTGGCCAGCATCATCACACAATTTGCAATAGGACCAGATAAAGTCCAAGTAG
Seq A exon
GTAGGTACCGTCTCCTTTGCCCTGCCCTTGCAGGGATGGGTGGGTGGGTGGTGGTGAGATTGGGTTTCTTGAGTTCTCACTAGCAGAAGGACAGCAGCTGCCCTCAGAAAAGGATAGTGACTGCTACAGCCTCTCAAGGTCCATCAACTGCCAAGAAAGTTAAGAAACCTGGCTGATAGAAGCCTGCTTGGTCTGAGTCAGGTCCTGACTCACTTTCTCTGTGAGTCTGGGCTGTCGTTATGGTCTGCAGGAATGGCTAGCTCCCAATTAGTCCCTCTGATGATATCTCTATGTGAGCCTTGGGCCCTGAAAATGTGTCATCTCCTGGGAGTGGGACTCCCAGAGGCTTTACCCAGAGCAGGTGATTCTGTGGATCAGGTTTTCAAAACTGAGCCTTGACACTGAGGATGTAGTAGCATACAACATGTGGCTAGCGTGCTTGCCTACCCCCCAGTGATGCAAAAAAGAAAGACCCCCTCCCCCAAAACCTCAATCCAGCAACCAAAGCCCACCCCTAG
Seq C2 exon
GTCTGACACAGTACAGTGGAGACCCCCAGACCGAGTGGGACCTGAACTCCTTCCAAACCAAGGAGCAAGTGCTAGCAGCTGTACACCACCTCCGCTACAAGGGAGGAAACACATTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-Col20a1:NM_028518:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.052 A=NA C2=0.073
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(23.1=74.1)
A:
NA
C2:
PF0009223=VWA=FE(23.1=100),PF0385310=YjeF_N=PU(3.0=7.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACCCCCAGTTCCAATGTACA
R:
CTGTGAATGTGTTTCCTCCCT
Band lengths:
278-796
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: