MmuINT0039734 @ mm10
Intron Retention
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:63254289-63254741:+
Coord C1 exon
chr4:63254289-63254342
Coord A exon
chr4:63254343-63254696
Coord C2 exon
chr4:63254697-63254741
Length
354 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAG
5' ss Score
4.95
3' ss Seq
CCCCCATATTTCTGTTTCAGGGG
3' ss Score
11.5
Exon sequences
Seq C1 exon
GGGCAGCCAGGACCTGAGGGCAGTCCAGGGGCCAAAGGTTACCCTGGCAGGCAG
Seq A exon
GTGCAGTATATGCTCTGGAAGCCCTGCCCATGGTGGTGGCCACAGTGCCCCAAGGAGAGGGAGGATGTGGGCTGGGGCCAATAAACTGCCCCTGGGGGCAGACCCTAAGGAAAGGGCTGGCCAGGGACTAGACCTGGCCACAATGCTGCAGGCTCAGAGGTTCTACAGGAGAACTAGGGCTTAGAGAAGGGGTTCCCAAGACTCCTCTCCAGTCTTGCCCTGAGTCACCTCTGGTTCAACCCATACCATGGATGTTTCTAAGGACAGCTGAAGCCCAAGATAAGACTGGCCCTGGGACATTGGCAGCAGGGAGGGCGTCTCCATATGTCCTCGCCCCCCATATTTCTGTTTCAG
Seq C2 exon
GGGTTCCCTGGACCTGTAGGAGACCCTGGCCCCAAAGGCAGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672:ENSMUST00000036300:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(19.5=100),PF0139113=Collagen=FE(22.1=100),PF0139113=Collagen=PU(10.4=38.9)
A:
NA
C2:
PF0139113=Collagen=PD(5.7=33.3),PF0139113=Collagen=FE(18.2=100),PF0139113=Collagen=FE(20.9=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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