MmuINT0038956 @ mm9
Intron Retention
Gene
ENSMUSG00000032332 | Col12a1
Description
collagen, type XII, alpha 1 [Source:MGI Symbol;Acc:MGI:88448]
Coordinates
chr9:79521864-79522627:-
Coord C1 exon
chr9:79522488-79522627
Coord A exon
chr9:79521994-79522487
Coord C2 exon
chr9:79521864-79521993
Length
494 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTTTTTATTTTCCCTTCCAGTTT
3' ss Score
11.45
Exon sequences
Seq C1 exon
GTGACTTGGAAGCACCGACTAACTTAGTAATTTCAGAGAGAACTCACCGTTCTTTTAGAGTGAGCTGGACACCCCCTTCTGACAGTGTGGACAGATACAAGGTGGAATACTACCCTGTCTCTGGAGGGAAACGCCAGGAG
Seq A exon
GTGAGCAGGTGACCCTTAAGCACTTCTTCCCTATAGTGAAGACTGGGTGAGCCTCATTAGAGCACAGAGGAAAACGTTGGGTGAAAGACAAGAGATGAATGAAGAGTGGTACTCTGTTCCTCTCAAGACAGGCACTTCTGTTTGGATCTCATTAAAGGGAAATAGCTTTAAAAAATGTTCTTAATGGTTTCTAAGTACTGTAGAATATCAGTCCAAGTTTTCAAACAAGTTAATTGATTCATAAGTTTGGACTAGACTCATAAAGTTGACAAGGGAAACTTACTAGAGATGGCAAATTGTACTACTTCTACAAACATGGATATCATAGCTGGGAAAATAAATTACATTGTCACCTGAGATCGCTCTGTAATCCAGTAATTTCTCAAAATAAAGGGCAAAGTCTCCTGGGATACCTTCTAAACCTCCTGGAGGTGGCTGTTTGGAGGTCTCTCAGGAAGAACGGAGTTGAGCATCCTTTTTATTTTCCCTTCCAG
Seq C2 exon
TTTTATGTGAGTCGACTAGACACTAGCACAGTGCTGAAGGACCTGAAGCCTGAGACTGACTATGTGGTGAACGTGTACTCTGTGGTTGAAGATGAGTACAGTGAGCCTCTGAAGGGCACAGAGAAAACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032332-Col12a1:NM_007730:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.128 A=NA C2=0.091
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.8=79.5)
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:
GTGACTTGGAAGCACCGACTA
R:
GGGTTTTCTCTGTGCCCTTCA
Band lengths:
270-764
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: