MmuINT0039474 @ mm10
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:181015690-181016332:+
Coord C1 exon
chr2:181015690-181015857
Coord A exon
chr2:181015858-181016254
Coord C2 exon
chr2:181016255-181016332
Length
397 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCA
5' ss Score
7.22
3' ss Seq
AATGTCCCCTTTCCTCTCAGGTG
3' ss Score
11.32
Exon sequences
Seq C1 exon
CACATGTGCTGAAGCTGAATTCCTTCCTCCATGAGAATGCCCGTCCCCCAATGCCCTTCATGGCAGAGACAGCTAAGCTAGGCAGACCCAGATCTATAGATCCTGGATTACACAACGAGGCTCTACTTCCTGGAGACTGGGGACATATCCTCCGCCCTGAGGACCAAG
Seq A exon
GTATCAGGCTTCCTGCTTTAGGAAGGGACTCTAGAATTAGACAGTGGCTGGTTCCCTGCACACACATGGGTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCATGCATTTAGAAGTTGTAAAGTCTCTGCTCTGGCTGATGAACCCACACTAAGGTACTTGCTTGGGACTCAAAGACCCGATGTGCTGGCATCCTGAGTGCTTAGCCTTAGGCCAAGGGTTGAGCCTCATGCTTCTCCCAAGAGGACCCAGCCTTCCTCTGACAGACAGGTCAGAGAACAAGAAGCTGAAGCTGCTACGTCCCCAGTCCTGGAATGTCCCCTTTCCTCTCAG
Seq C2 exon
GTGAGCCTGTGACTATCAGCCACACAAGCAACCCTAGACTGCAGGAGGTGCAGACCCCAGAATCCCTGGAGTGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356:ENSMUST00000108856:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.912 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACATGTGCTGAAGCTGAATTCC
R:
CTGCTCACTCCAGGGATTCTG
Band lengths:
246-643
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