MmuINT0038949 @ mm10
Intron Retention
Gene
ENSMUSG00000032332 | Col12a1
Description
collagen, type XII, alpha 1 [Source:MGI Symbol;Acc:MGI:88448]
Coordinates
chr9:79680293-79681581:-
Coord C1 exon
chr9:79681389-79681581
Coord A exon
chr9:79680415-79681388
Coord C2 exon
chr9:79680293-79680414
Length
974 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
TCTGCATATCACTATTTCAGGGC
3' ss Score
8.72
Exon sequences
Seq C1 exon
CGTCTCGATTTAAATCGCCGAGAAACCTCAAAACTTCTGACCCAACCATGTCAAGTTTCAGAGTGACTTGGGAGCCTGCCCCTGGGGAAGTGAAAGGTTACAAAGTCACATTCCACCCTACAGGCGATGACAGAAGACTTGGGGAGTTGGTCCTTGGACCATATGACAACACAGTTGTCTTGGAGGAGCTTAG
Seq A exon
GTAGGAATGAACTGTATTTGTGCTAAGGACTGTATCACTTAGGTAAATTTAAATAGGCTTTATACAAAGAACAACCTCACGTGTTTGCAGAAAACAGAAAAGAATTAAGTCTGACAAACAGCTTGTATTGTTTAGATAACTTTTGTTACTAAGTGATCAGGGATGACTTTTAAAAAGAATACCTGGGTTTTGACATGTCCGTATCACATAGTTTCATTACAGTTGCAGTCATGTGAAAATGTGTGGCCAAGTGACTCATTCTGAGACACTCCCCTGCCCCCGCCAGGGTGGATGTCCCTGCAGGGAAGCACACTGGAGCTCAAAGGCCAGAGTCTGTGCTTGTGGCCAGCTGGCAGAAGAGCTTTGAGTTGATTAGAGGTCTAGTTTTAGACAGTGAGATGGAAAACAAAGGAGTGTGAACTTGAACAGCACTCCACATTCATCCAGAGATACCAATGGGTTACTGTACATTCCTCTTGGAAACTTTGCTTGCTCAAGTATTCATTCAATAGTGTTGGAACCTGTATAATGCTTGCTGTTCATTGTAACTTGAGTAGGTAGGATGAAATTTGGAAGGTCACTGTTTGACATTGCCCAGTGCTGAGTGTCTTAGGTCATTGGGCAGACACAGAACATTTCAATCATTCTAAAGCCGGCATCTCAGGAGCAGCCTAAGCAGGGCAGCTAATTTTTCCCAACACTGAGCGGCATGGGGGAAATGCTGTCTCTCTGACCAGTCCTGAGACAGTGCTGTAAATCCCCAGAGCTCCCTGGAATGCTGGGTGGCTAGTTTCCTGTGATTCCTTACCAGCAAGCTGGAATGTGATGGCAACTATCTTTCTTCTTTCACAATACTGAACATTATTCATTCCTATGGGTGAAAGTTTGTTAGTGAAGATAAGTTATCTTTAACAAGATGGAAGCTGTTCCTTTGAGACCATAGTCCCTACCCACTCTGCATATCACTATTTCAG
Seq C2 exon
GGCAGGCACCACCTATAGAGTCAATGTTTTTGGGATGTTTGATGGAGGAGAAAGTTTACCACTCGTTGGGCAAGAAATGACAACTCTTTCTGACACAACTGTGACACCATTTCTATCTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032332:ENSMUST00000071750:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.385 A=NA C2=0.071
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(74.1=92.3)
A:
NA
C2:
PF0004116=fn3=PD(24.7=47.6)
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:
ATCGCCGAGAAACCTCAAAACT
R:
CAGAAGATAGAAATGGTGTCACAGT
Band lengths:
302-1276
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