MmuINT0039394 @ mm9
Intron Retention
Gene
ENSMUSG00000001506 | Col1a1
Description
collagen, type I, alpha 1 [Source:MGI Symbol;Acc:MGI:88467]
Coordinates
chr11:94801218-94801485:+
Coord C1 exon
chr11:94801218-94801271
Coord A exon
chr11:94801272-94801431
Coord C2 exon
chr11:94801432-94801485
Length
160 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
GCTTCTCCTGTCCCCTCTAGGGT
3' ss Score
10.93
Exon sequences
Seq C1 exon
GGTCCACAAGGTTTCCAAGGCCCCCCTGGTGAACCTGGCGAGCCTGGCGGTTCA
Seq A exon
GTAAGTTAGTCCTCCATGCCGACACACCTCCATCTCCACAAATTCTCCTATGGAAAGTCACCTGTACTGAGAGAGGGGTAGCTTGTCACCTCCTCGCTCCAGTCTTCCTCCTTATTGTCTCTCATCTAAGAGTTCTAAATGCTTCTCCTGTCCCCTCTAG
Seq C2 exon
GGTCCAATGGGTCCCCGAGGTCCCCCTGGCCCTCCTGGCAAGAATGGAGATGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001506-Col1a1:NM_007742:8
Average complexity
IR-S
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(27.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.4=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:
GGTCCACAAGGTTTCCAAGGC
R:
CATCTCCATTCTTGCCAGGAGG
Band lengths:
106-266
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: