MmuINT1007478 @ mm10
Intron Retention
Gene
ENSMUSG00000048126 | Col6a3
Description
collagen, type VI, alpha 3 [Source:MGI Symbol;Acc:MGI:88461]
Coordinates
chr1:90796480-90798197:-
Coord C1 exon
chr1:90798052-90798197
Coord A exon
chr1:90796573-90798051
Coord C2 exon
chr1:90796480-90796572
Length
1479 bp
Sequences
Splice sites
5' ss Seq
CTTGTGAGT
5' ss Score
7.15
3' ss Seq
ATTTACTTTTTCCTTGGCAGGAC
3' ss Score
9.72
Exon sequences
Seq C1 exon
GTGCCCAAGCCCTGATCCTGGTGGGTCTTGAACGTGTGGCTAACCTGGAGCGGCTGATGCATCTGGAGTTCGGGCGGGGCTTCATGTATGACAGGCCCCTGAGGCTCAACCTGCTTGACTTAGACTATGAACTGGCAGAGCAGCTT
Seq A exon
GTGAGTCTTTGTATCTTTTAAAGAGTTTTACACACACACACACACACACACACACACACACACACACAGAGAGAGAGAGAGAGAGAGAGAGTTTGAAATTTTTGGCATCTCAAGACAGCAAAGCCAGATATCTTACTGGCCTGGTGACTGGGGGAAGGGCATATGGATTTATCACGGACTCCGTCAAGGCTTGCTTTATTGCTGTATGAGTCCTGAATATGCCATCTGCCTTTCTCCATGATGGAATAGAGAATATGCAGGGAAAGAGATGGAGCCAACTTCTAGGTGAAGTCCTCTCCCTGGCTCCCTTTCTGGGCTCTTCTCTTAGTGAGAGCCGTTGCCTCCTGGGATGGGGAGTTGGGTGGGAGTGTAGCCAGGGATTCTCAGATAGTGTGACTAAGGCTGTAGGAGTGGGAGGGAGTGCTGCCCTCTCTTCCTCTTTCTGTATTAAAAATTGGGGTGTTTTTATTGGGTAGAAGCAGCTTCAGGCTAGAACAGGGGAGAACGCACACAGTCAGCACTAATTCAGTGAATGGCACTGTGTTTGGGATGTGTAAGGTCAGGGGCTTGGCAAGGGAGGGATACAGAGGTGGCTGGTGACCCAGATTGTGGAGGTCCTGGCTCAGAGCCCAGGGCCCCACGTGCTGCCTACCCCTGGCTTCTCCAGGGACTCTCTCAGGCCAGTCCCGATTTCCACCATCCCAACTGTGGCTCAGAGAACCTCAAGGTGTAGATTTCTAATTTAGAATGCTCTTTGACCTCAGGTTGCTTCAATGTGTTGGTTGGATTTTATATTTGAGGTTTGGACATGAGGAGGTTGTCTTAGTTAGGGTTTCATTGCTGTGAAGAGACCCATGACCAAGGCAACTCTTATAAATGACAGCACTTCATGGGGGCTGGTTTACAGTTCAAGAAATTCAGTCCATTATCAGCAAGGCAGGGAAAATGGCAGTGTGCAGGCAGGCAGGCATGGTGCTGGAGAAGGAGCTGACAGTCCTACACGTTGGTCCACAGGCAGCAAGGAGGAGACTGTTACTGAGCAGAGCCTGAGCATAGGAGACCTCAAAGCCCACCCCCACAGAGACACACTTCCTCCAACAAGGCCACACCCACTCCAAGAAGACCACACCTCCTAATAGTGCCATTTTTCATGGGCCAAGCATTTAAACATGTGATTCTATGGGGACCATGCCTATTCAAACCACCATAGAGGTTATACTGAAAATCCAAGCCCTGAATGTCTGTATTAGAAACGTCTGGAAAATGAGCCTAGTCTAGGATAAGAATGACCATAGTTGATTTTTCTTTTCTCTTCCACCAATGACTTCCCACCCTATGGGAAGAGCTGAGTCCTCAGCTGTACCTGGCCTTTGAGGGAGTGGCATGAGGTAGCTCACTGCGGCAGATTAGGACTAATCCCAGACCCTTGGTGGTTCCCTGTTTTCTCTTTTTGATATTTATTTACTTTTTCCTTGGCAG
Seq C2 exon
GACAATATTGCTGAGAAAGCTTGCTGTGGGGTTCCATGCAAGTGCTCTGGAGAGAGGGGAGACAGAGGGCCCATTGGCAGCATTGGGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000048126:ENSMUST00000097653:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.355
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(25.8=51.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCCCAAGCCCTGATCCTG
R:
CTTTGGCCCAATGCTGCCAAT
Band lengths:
238-1717
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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