MmuINT0039421 @ mm9
Intron Retention
Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4478306-4479121:+
Coord C1 exon
chr6:4478306-4478413
Coord A exon
chr6:4478414-4479067
Coord C2 exon
chr6:4479068-4479121
Length
654 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCA
5' ss Score
7.87
3' ss Seq
CTCTTGCTTTGTACTTCCAGGGT
3' ss Score
8.91
Exon sequences
Seq C1 exon
GGTGAAGCTGGTGCAGTCGGTGCTCCAGGCAGTGCTGGTGCCTCTGGGCCTGGTGGGCTTCCAGGAGAGAGGGGTGCTGCTGGCATACCTGGGGGCAAAGGAGAAAAG
Seq A exon
GTACCACTCGGTGTTAGACCTTGATACATAATATCCATGAACTCCAGGCAAGAAGGCTGTGCGAGGATGCACAGTTGTTTACCATTCATAGCAGGCGGTCTGGTAGCATTTTGACATCTATATGCACCTCCCTCTGCCACCCAGCACCTACACATGTCTAAACTCACTAATCTGGCAAAATTCCTTGCTACCATGGAATTTCATGCAAGCAGATGGTGTTGAGTAATACATGAGGCTCATTTTAATGCCACTAACAATAATGCCTCATCCTGCCCTAATTAATGGAAGAAGCTATATCAAACAGCTGTTCACCGTGCTATGGCATTCATTATGTTATAAGAGTGACCGGGCACCACAGCCCGTCGCCATGTTGTCTTGTGATTCCAACCTCATCAATTTGAAACTTGCTTCGTGATGAATCAGAGGGATGTTTATTTTTTAGTGTTCGGTAGTCCTCTGAAAGGGGCCAGAAAAGATGAACTTCCGACTGTTTTTCTCATTCAACATCCTACAAAGTGGTGGGAAACTGAAAAACACTGAAATTCTAAAAGGGTGGCCAGCATTATAGAAATTTTTGTCAAAGCACTTTGCAGTTCATTTCCACTCAGAAGTTGAGCAGGAAAGCAAAATGTGGCTCTTGCTTTGTACTTCCAG
Seq C2 exon
GGTGAAACTGGTCTCCGAGGTGACACTGGCAACACTGGTAGAGATGGTGCTCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029661-Col1a2:NM_007743:32
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=PD(23.6=47.2),PF0139113=Collagen=FE(47.9=100),PF0139113=Collagen=PU(42.0=80.6)
A:
NA
C2:
PF0139113=Collagen=FE(23.0=100),PF0139113=Collagen=PU(12.5=61.1)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: