MmuINT0038955 @ mm9
Intron Retention
Gene
ENSMUSG00000032332 | Col12a1
Description
collagen, type XII, alpha 1 [Source:MGI Symbol;Acc:MGI:88448]
Coordinates
chr9:79522488-79525111:-
Coord C1 exon
chr9:79524965-79525111
Coord A exon
chr9:79522628-79524964
Coord C2 exon
chr9:79522488-79522627
Length
2337 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
TCTTTTATCTTCACACACAGGTG
3' ss Score
9.69
Exon sequences
Seq C1 exon
GTATTAAGAATGCTGATGAAGTTGAGTTAAAGATGATTGCCACTGATCCAGATGACACTCACGCATACAATGTGGCAGATTTTGAGTCATTGTCCAAGATTGTGGATGACCTCACCATCAACTTGTGTAACAGTGTCAAGGGCCCTG
Seq A exon
GTGAGCTTGGTCAGATGCTGGTGTGTCTGGGTGGGGACCCTCTCATGTGCCTTTAGAGGCTTCTGCCTCCTCGATACCAGGAGATTCCCCTGAGTTGTGGTGACTAAAGATAACAGGGCAATTTTTAGTATCTGCATCTGGTACATGGTAAATAGTTGAAGGCTTTGTGCAAGTTAATTAAGAGACTTGGTCCTTATTACATGTGAAATTTTTTCTTTTTATATAGGAATATTAGAGTAAAACTTCCCTCCGTTAATTTATTTTGGTTCTGGGAAAGTTAGAATGAATTTAACCTCATAGACACAGTAGAAATGGTTCCAGATGTTTGCAGAATTGCCATTACTAGTGCTAGATGTCTGCTTTGAGGAACTTCCTAGTTAAGGGACACTGCTTTAGTTCATTTTAAAATGATTTTTTTTCTTTTTTTGGTGGCGGGGATGGCACCAAACTAAGAAATGGCTTCTAGCTTATTTAAGGATTTATTTAGGTTATATGGCTTAGTTGATGCAAACAAAAGTGGGAAGAGACAAAATAATGGAAAGAGAGTTGACAGACACTCCTATTCTAGCACAGACCTGCTTGGGGGCAACACAGCTTCACTTCAGTGCTACGTTATTCAGACAGCTATGACTTAAAAGTTGACCAATTTGGCTTGCTCAGTAATGTTTGGTAGCTTTTTTTTTCGGCTTCCTAATGTATAGGGGAAGACATCTTATGTCTGATTTCCTTTCTTCAGCTGCAGATTTTCAGGTCTGATGCTCTGCACTGATAATCCCCAAATGTGAAGAGAAGTTACAGCCTTAAAGCTTAGACCATACGAAATCACAAGAAGACATAGACCTAGAGCAGTTACCTAGTTAGGGTCAGATAGATAGGGGTGCTGTTGTGGGACTTTGCATGATGTAACCATGGAAAACAGATTATGGTTTAGAAACAATATCAGAACTGGGTTTGTAGTGACAGTGGAGGGCATAGAATGGTTAATCTCTGTGCAAACTGTAGGACAAGACAATGGAAGTGGCAATACTGAAGGGCTTTTCAGAATTAATGACAGATCCATGATTCTTAGAGTGTGAGGACATTTCCCTTAAACATGTGGATTGTGTAGAAGCAGTGTGTCATTAGCTGACAGTGGTTTCAGAGATGCGGAATGAACTCTTACAGTGTGGCAGAAACACTTTTGAAGGTCTGTGTCCTTGGTTACATCCACGCTGCATATTTCATGTTCTTTCTTGTACATCTGTCTTCAAACTTTTGCAGATATTCTCTTTTGAATTTTGAACAACAGACTGGCCTTTTCCCTGGAGAAACAGACCAGCTGGGCAGCCAGAATTTGTAGGCTTCTGGCTTTGGGTGAACTGAGAGAATTGTCTTTTTTTATTCAATTGGAGTGAACTTTGAATGGGGATGGAGACATCTTTTATCTGTTTTTTTTCTTTATTGTTTTTTTATCAACTACGTAATAGTTGCAGTCATTGAAGTTTCCCAGGCCATAAAACAACTTGATAATTTTGCAAGCTTGATTTCGACCCAACTGCTAAGAGCAGACATACTCACTCAATTTGGGCTTACAAAGAAACCCAGAGGAGCATGTATGAAAGTGATTTGTCATGCTCATGGTCACATAAGAGCAACTCCTCTCTCTTTAAATCATTATTTGTAACAACTGGCTGTTGGTCTTAATGTATTTATCACATCAATTTTTAATTTTCTAGTTACTGTTACACATTGTTTTACCCATATCTTCCCACAGGAAGCACAACCACAGGCTATTTAAATATGCCTATAGCCATATTTTAAAATATTGATATTTGCTAGTTTTCATTCTTTTTAAACACATAAGAAATAAGTGCTCTAAAGACACTCAACACAGACAAGCCACTAGTGTTATCTTCATAGAACACAAGATGTGTAGAAATGGTAATGGGGTAGGGAACTTGGTCTAGCCTTAGACCATGGAAAAGTAGAATTGTCTGGATTTAGGTCCTGTTTATTAATTATGTAGAAGGGGTTGAGAGAGGAGAGGGCATGAGAGATGACTCAGAGGTTTTGTGTCTAGGTGACATTTTAACTAGTGGTTTCAGAAAGAACAGGAGATCATGTTTAAAGAAGGACAAGGCACTCTGGTTTGACGCTTCTGAGACTAAAGGAATCCTTTAGCCATTTGTTCAGAGAGACCAATGGGCAATGGGCTTTCGTACAGATTCATCATCTACTTTCCATGTTAAAGGGAGCCTGTGAAAACTTCTGTATAGACCAGCACTCTTTCAAGCTAACTTCCTCCTTCACCACTTTCCTCCAGAAATGAGAGTGTGTATCTTTTATCTTCACACACAG
Seq C2 exon
GTGACTTGGAAGCACCGACTAACTTAGTAATTTCAGAGAGAACTCACCGTTCTTTTAGAGTGAGCTGGACACCCCCTTCTGACAGTGTGGACAGATACAAGGTGGAATACTACCCTGTCTCTGGAGGGAAACGCCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032332-Col12a1:NM_007730:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.128
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=74.0)
A:
NA
C2:
PF0004116=fn3=PU(53.8=91.5)
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:
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: