MmuINT0038950 @ mm9
Intron Retention
Gene
ENSMUSG00000032332 | Col12a1
Description
collagen, type XII, alpha 1 [Source:MGI Symbol;Acc:MGI:88448]
Coordinates
chr9:79526268-79528221:-
Coord C1 exon
chr9:79528100-79528221
Coord A exon
chr9:79526418-79528099
Coord C2 exon
chr9:79526268-79526417
Length
1682 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TCTTACCGTTGCCATGTCAGGGA
3' ss Score
6.13
Exon sequences
Seq C1 exon
GGCAGGCACCACCTATAGAGTCAATGTTTTTGGGATGTTTGATGGAGGAGAAAGTTTACCACTCGTTGGGCAAGAAATGACAACTCTTTCTGACACAACTGTGACACCATTTCTATCTTCTG
Seq A exon
GTAAGAAACTGAGTTATATTTCCATGAGAAAATAGTATTATGAAACTATCGGGCAAGTGAAGTGTGAGGCTATTAAGCAATGAAAATTATAACTTTCACTACAATTTATTTAAATAATGACAAACTCTTTTATATTTGTAGAAACTGCTTCAAATATCCAGTTGAGCCTACTTTTTTCGCTTTTCTTTTTTTTCAATTTCGCATTAATTAAATACTGGATTATTTAAAAATGAGTTTTTATTAAGTGTAACTTTCTATTTTTTCTTTTTTAGTAATGTGATTTTCTTTTATTAAGATAGTTATATATTTTTTACTTTGAGGGCTTACTTGGATGGAGAAAGAAGGCTCTATACATAAAGAATCGGGCAAGCATGACTTACAAGCATGATAGTAGCACAGCCCTTTAGAGGTTTTGTATTTGCCATAATTACAGCTTTGATGTAGGCGAGCCAGCATTTAATAGAATTAAAGGTGAGAGTAGGAGATAGAGTTTCCTTCTAAACTTTAAGAAAAAGTGCTTATTAAACCCAGTAGGTCTTAGCATAATCAGAGTAGGCTGTAAAGATGTAGGTTCTAGAACAGTACACAGCATCTTCCATTGTGAGAAAGGCTATGCACAGATGGTACTTCTGTAATTAGCAGTGTGATGAACATTGCTTAATTTTTGTTCACTTTAAAAGTGATGCAAATATGATCTGATAACATTGCAGTAAATGAGAAAGTTTATAGGCTGCAAGCTTCTAAAAAAAAGAACGTTTACAATTAAAGGTGGATAAAAGAAAGTGTCAAAATTTGATATTTTGCATTGTTTCATTGTTTCTCTTATGATGATATTAACCGGCTTATATTTTTATTTTGTAGCTTGTCACTGAGGATATTGGGATTATTTTCTCTTTCCAAAGCCCCTTAGCTTTGTATCTGTGTTTGCGTTCGTTGTCTCGACAGCTCTCAATTTGTGTATTTCTCTGCATCCTTTCCCAAATTGTCTTCCTTCTTCCTCAATTCTTTAAATGTGCAAACTTTGCTGTCTGAATTTACCTAATTTTTATCTGCAGTAGGTGAAAAACTTGAACAGTTAATAATGAGATAATAGAATAGTGTTTCGAGTTTTCAAAACGTGTCTTTACTTCACAAAGGTCTGATTTTAAGACTCATGTATCCAGTCCTCCATAACATGTAATGGTTACCTGGTGGCTTAATTATTATAAAGAATATTTTTGGCTCACTGGAATCACTTACAGTTTAGACATTTAACCAGTCCATCTTATGCTTATATGCTAATGTCTTAAAGAGTGAAGGAGGATGCTATATCTTATAGCACATCCACATCTTATTCAAATTATTAATATTTGTTGTTAGATAGCTATGCATTCTCATTTATTATTTTAGGTATTGATTGTGTGAGCCTTTCAAACTAACCATCATAGTTTAACTAAACTCTCTAGGGTCTATGGTTGTGATCACAATATATATATATAGTCACCAATGGAGAAGAGGTTTGCCACTGAAATGATATTTGGAGAAAGGGATTCACATGAATATCATTTAAGGTTAATAAATTATAGTTGGGTCTTTAAATTATGACACCTAGCTGCAGTGTTAAATAGACAACTTAGGTGGCACAGGGGACAACCTACCAACTATGTGCTTCTTATCGTCCTGTCTTACCGTTGCCATGTCAG
Seq C2 exon
GGATGGATTGTCTCACCAGAGCTGAAGCAGACATTGTGTTGCTGGTGGATGGGTCATGGAGCATCGGCCGTGCAAATTTTAGAACTGTGCGAAGCTTCATTTCTCGTATTGTAGAAGTCTTTGAAATTGGCCCCAAAAGAGTACAAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032332-Col12a1:NM_007730:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(24.7=47.6)
A:
NA
C2:
PF0009223=VWA=PU(23.1=78.4)
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:
GGCACCACCTATAGAGTCAATGT
R:
TTTGTACTCTTTTGGGGCCAA
Band lengths:
265-1947
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: