MmuINT0040445 @ mm10
Intron Retention
Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:106020766-106022924:-
Coord C1 exon
chr9:106022874-106022924
Coord A exon
chr9:106020802-106022873
Coord C2 exon
chr9:106020766-106020801
Length
2072 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTTATCATTTCTGACCCTAGGGT
3' ss Score
9.04
Exon sequences
Seq C1 exon
GGTCTTTTCGGTCCAGACGGCCATGGTTATCCGGGAAGAAAAGGCAGGAAG
Seq A exon
GTGAGCTCCTGCCAAGAGCATTCCAATATCAAGTCACGTTCCGAGTTTTACTAGAATATAGTGACTGTATGTCAGGAATGGTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCTTCCTTCCTTCCTTCCTTTTTATAGCTTGACAGAGTTCCCTTACTGAGAAATCAGACTGGGCTCATCCCTCACTTCCCTGCCTTTCTCCCTTCACATTCTCTATACTCACAGGCTCCCAATGATAGATTCAACCAGCTATAGGTTAAGACATCTGAGAAAAATCTGCATGTGTACTGAACATGTACGAACCCATTATCCCCTAAATAGCTCAAGGTGATGTCTGTTTCACAGCACCCGTAGTTGTAGGTGTTCTGTGTCATCTGGAGACTAAAGTCTAGTAGAGGGTGTGCATATGTCACATGTATGTGCTTGGCAGCACCGTATTACGTCAGGGCGTTGACTGTGCTCAGATTTCTGTACCTTTGGGGGATATTGGAATCAACCTTCTGAAGATATTGAGGGGCAGCTGTAATTCTTTATTTCTTTTAAAAATACATAATATTTTAACTTTTTCTTTGAGAATTTCATACTCTCATTTTATTCCTTCCTCCTATCTCCCCACTCCAGCTCCTTGATCTCCTTCTGACATCGTCTCCTTTCCAAGTCTTTAAAACTTGCTAAGTCTGATTATCCCTGCCCATATGTGTGTGGGAGCATCTACTGGAGTTATAATTTCTAGGTGGTGTAGGGGGAATTGTAAAAACTATTTATGGATTGTCGACCTCTGGGATTGAAATGTGGCCTCTTGATGACCTTTCTCAGAGGAATGTTGAGGAAAATGTATTCACTGGTCATTGAACGTTATATAAACATGTCCAATATATAGAGAGCTGTATACCTAATGAAAACTGGTTTTCCTTCTAGCGGCCATCAACTTAATAATTCCTCAGCCCTGAATATCTTTTGCAGGAAGGCTTTATAGAAAGCAGCAAGTGGGAGGTGAATGTTTCTAGCCTGGCAAGCATCTAATTGGAGAGCACCTATGGCCTGTAGCATAATTGGCTGGTGCTGGGAGTCAAACCATAAACTTAATTTCTGCTTCCCTCTGCATTGGTGGTTGTTATGCAGGGGGCAGGCTTGTTGGCAATTAACTTGGAAATGCTGGATTGTTGGGGAAAACTAACCTGGAGATGCTGGTCTGTTGGAGTTAGCCTAGAAACTGGAGCTAGGCTTGGGTTTTGTTGTGGGGTAATTTGGAAACCAATGCTAGGTACCGACCTGTTAGTTTACCTGAGTTCAAGTTTTCTAAAATGGAGTCTGAACTTAAAAGATTTGTTCTCTCACTCTAACATTTACTTATTTGTGTGTGCAAGAGCATAGGAGAGTGGACTGCCTGCTCGATTTGTTTTCTCCCTCTACTACCTTTGGTCTCAGGGACTGAACTCAGGTCGGTAGGCTTGGTGGTGAGTGTCTTTCCCCCACAGGACCATCTCACCAGCTCATTTTTAATTTCCTGGTCCCCACTCTGGAATCCTGGTCCATTTCTGAGATGCTATTTACTTCTTTGGTCACTTGCTTCTTTGGGAATGCAAGTTCAGTGTGGGTCTTGGTTTTGTGCATAGCTGAGTCCCCAGTGATTACAGGACCACTTGGCAAACAGCAAGGGATAACTAAATGTCTGTGGGATGGGCGATCATTTTGAAGCATGCCTGTGCCTCTGACGGTTCCATGCTGGGTCCTAACATTCAGATTGATGCTCCTGCCTTGCTTTCTGTTGTCACAGATCTCAGGGGCTTTAGACTGAGAAATAAAATGCACAAGAAGGAAGTTTCATTAGACCCTGCATCAAAGATGCTTAAAATTGTAAAAACTATTTATAAATTGTTGATCTCTGGAATTAAAATGTGGCCTTTTGATGACCGTTTCTCTTTCCTGGAGGAATGTTGAAGAAAAACTTAAATTACCTGGCACTGAATGTTTTCTTATCATTTCTGACCCTAG
Seq C2 exon
GGTGAACCTGGGTTCCCTGGCTATCCTGGTGTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572:ENSMUST00000121963:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(21.3=100),PF0139113=Collagen=PU(12.3=47.1)
A:
NA
C2:
PF0139113=Collagen=PD(12.0=75.0),PF0139113=Collagen=FE(16.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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
- 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