MmuINT0038986 @ mm10
Intron Retention
Gene
ENSMUSG00000032332 | Col12a1
Description
collagen, type XII, alpha 1 [Source:MGI Symbol;Acc:MGI:88448]
Coordinates
chr9:79703631-79705621:-
Coord C1 exon
chr9:79705562-79705621
Coord A exon
chr9:79703895-79705561
Coord C2 exon
chr9:79703631-79703894
Length
1667 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
ATTTGTCAAATTCATTTCAGAGT
3' ss Score
7.43
Exon sequences
Seq C1 exon
TTCAAACAGGTGGTCCTACAAAGCCAGGGGAGAAGAAACCTGGAAAAACAGAAATACAAA
Seq A exon
GTGAGTTTCTTTCTGTATTTTTGCTTGGATTTGTAGAAGTCACAACTGCACTGTAGTAGATGTTCTAATTATAGACAAAGCTTAATCATATTCCCTATGTTAACAGATATAAGCTTTCTCTAGAAGGAGTAGATAACAGAGAAATGTATAACTAAATACTTATAAACCTTGAGGTCTTCCCCCTCCTATAAATTGATAGCAATAGATGGTACTTACAGATATATGGGAGCAGACTCAGAGAATCTTAGTAGTTGAAGCAACTCAAGTGCTGTGAAATACACTTTAGGTGTACTTGCATATTGAACTCATCCCTGGGATATTTCTGTTACCTTGGCTCATGACGTCAGCTTTCTCAATCTTCCCAGAGTTTCTGCAGCCCATCCATCTCTAAGGACTTGGTGAATTCATAACCAGATGAAAAATACTTTTATTTATTCCGGCTGTGAGGCTCTTCCCCTCCATTGTCTGACACTGCTTTGCGTGGCTTGCTAGAGTGAACTCCCAAGGAGTTTCTTGGACGTCTGATTTTGCCACTTTGTAAGCTGGATTTATGACCCAGACTGACCATAAAAACATTATAAACACAAAGGCCTCTTTCTCTGGAGCAGTTCCCTCTAGATCACTGTTTATCATTTCCTCAGATGTCCAATAATCTAAAATGAAGTTTCTCTTATGCAGTTATATTAATATTTTCTCCAAACTATCAATATTTATTCTAAATCAAAATATTCTGCCAGATATGGGTTTTTAATAGACTAAAATTGCCCTATTAAACAGCATATAATTGTCTTGCACAATTTTCCAAGACCTTTTCCTGCTCCTCTTTGCCAAATACTTTTTTTTATTATCTACCAACTAACTTCAAGGACAAAAACATCTTCAGAAATCCACTAAATGTTGCCTTGCAAATATGGATTTTCATGAAAACCAACTTGCCTCCTTGACCACGGAAGAAGGAAATATAATGTGAGGTCATAAGAGTCCATTGCATTCTAATCCCTTAAGGATGCCATATGGACATTTGGGCTTTTGACTTACTAGTATTTCCTCCTTTTGTTTAATAGTGGAGATTTTAGTTGTCAAATTTGAGTGCATAGATAACAAAGACATAGATAGTTTGGCTACTTTGCATGACGTTATGCATAGACTACCCTGACTATAAACTTAGACGTTTACATTGGAAAATATGACAGACTATTAAAACATTTGCTCTGCTCTTCAACCCAGACCAAATCTGCCTGAAGAGCACAGATTGAATTTATCTGTTGATAAATAACAAAACGGGAGGAGACACTGTTGACATTTCTTTTGTGTGTCTCCCAGATGTTTTATGTAATCTTCATTTGGGGAAAATGAAAGATATGGTTCAGAAAAACAGGTTGTCACTGCATGTGCTCCGACTGCAGTATCCTGGGTAGCGTATCACATCTCTAGTCAGTTCTTTGCTATCGTGCATAGCAATGTAAAGGCATCCTGTCCCATACATGGATCTTCATATGTGCACTAAAATTACTTCAGTGTAATTTTAAGGTTGTATATCCTTTTAAGTGTGTAGATAGAAAACAGTGGGTCACATATATTCTAGTGAAGATTTTTGCAATGTTAGGCTGTGCTTTTTAAAAGACGGACTGATTTCATCAGTTAAAAATTTGTCAAATTCATTTCAG
Seq C2 exon
AGTGCTCTGTCAGTGCCTGGACCGACCTAGTGTTTCTTGTGGACGGCTCCTGGAGTGTGGGAAGAAATAATTTCAAGTACATTTTAGACTTCATTGTTGCTCTGGTGTCTGCATTTGACATTGGGGAGGAGAAGACGAGGGTTGGAGTTGTTCAGTACAGCTCAGATACCAGGACTGAATTTAACTTAAATCAGTATTACCGAAGAGAAGACCTCCTTGCTGCAGTTAAAAAAATACCATACAAAGGCGGCAACACAATGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032332:ENSMUST00000071750:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.714 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(46.2=89.9)
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:
ACAGGTGGTCCTACAAAGCCA
R:
TGTCATTGTGTTGCCGCCTTT
Band lengths:
318-1985
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