MmuINT0039452 @ mm10
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180999687-181000175:+
Coord C1 exon
chr2:180999687-180999816
Coord A exon
chr2:180999817-181000032
Coord C2 exon
chr2:181000033-181000175
Length
216 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
TTATACACCCCATCTTCTAGAGA
3' ss Score
5.96
Exon sequences
Seq C1 exon
ACTCAGGTTCCTGGGAACCTTACTTCAGCTACTCTGGGCCCACTTTCTTCCTCTACCATGTACACCGTCAGAGTCACCTGTTTTTACCTTGGGGGTGGTTCCTCCGTGCTGACTGGCCATGTAACCACAC
Seq A exon
GTGAGTCTGCGAAGTCAAGGCTGGGGTGCAGTTGGACTGTGCCCCTATGTCCTACTGAAGGGCCTATGTTGAGTGTCTGTTCTAGCTGTATTAGGGCAGGTGGGGACAAGTGTCTGGACAAGGGGCCAGGGACATTCCTCCATGTGGCCGACCCTTGTCTAAAAGTAAACGCTAAGGTCAGCACTCTATGCTCCATTTATACACCCCATCTTCTAG
Seq C2 exon
AGAAAGCTCCTAGCCCTGGCCAGCTGTCTGTGATGGAGCTCCCGGGAGATGCAGTAAAGCTGTCATGGCTGGCCACTGCCTTGTCTGGTGTACTTGTTTATCAGATCAAGTGGATGCCCTTGGGAGAAGGGAAGGCCCGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356:ENSMUST00000108856:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.341 A=NA C2=0.146
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.6=77.3)
A:
NA
C2:
PF0004116=fn3=PU(53.7=91.7)
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:
AACCTTACTTCAGCTACTCTGGG
R:
GGCCTTCCCTTCTCCCAAG
Band lengths:
252-468
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