MmuINT0040458 @ mm10
Intron Retention
Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:106074822-106077459:-
Coord C1 exon
chr9:106076872-106077459
Coord A exon
chr9:106075431-106076871
Coord C2 exon
chr9:106074822-106075430
Length
1441 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
TCTCCTTTCTTTACTTTTAGAGT
3' ss Score
11.44
Exon sequences
Seq C1 exon
CGTGCTCAGAAGCATCCCCGGCTGACATTGTGTTTTTGGTGGACAGTTCAACTAGCATCGGACTCCAGAACTTCCAGAAAGTGAAGCATTTCCTCCACTCTGTTGTCTCGGGGCTCGACGTCAGAAGCGATCAGGTGCAAGTGGGGCTGGTCCAGTACAGTGACAACATTTACCCAGCCTTTCCGCTGAAGCAGTCCTCTCTGAAGAGCGCCGTCCTGGATCGGATCCGGAATCTGCCCTACAGCATGGGGGGCACAAGTACCGGAAGCGCCCTGGAGTTCATCAGGGCCAACTCCTTGACTGAGATGAGTGGCAGCCGTGCCAAGGATGGGGTTCCTCAGATAGTTGTCCTGGTGACAGATGGGGAGTCCAGTGATGAGGTCCAGGATGTGGCTGACCAGCTGAAAAGAGACGGGGTCTTTGTGTTTGTGGTAGGGATCAATATTCAAGATGTCCAAGAGTTGCAGAAAATAGCCAACGAGCCGTTTGAGGAGTTTCTCTTCACCACAGAAAACTTCAGCATCTTGCAGGCGCTCTCAGGAACCCTCCTTCAGGCCCTGTGTTCCACGGTGGAGAGGCAGATGAAAA
Seq A exon
GTAAGCCCCGTTCAATCATCTACCACTGAACTGCAATGTAGCAGTGTGCTTCCGAAGGGGAAGGGTGGCCTATAATCACGGGAGCATCTGGGGATGTCTCCTAGAGGAGAGGAAGTCCGAGCTGGCCTTGAAGGATGAGTAGAGAGCTCATAGGTAGAAAAGAAAAGAGAAGACACGCTGTTGGGTTGTTTAGAAGAAACAGCATGGGCTCTGGGGTAGAGAAGTCATACTTTTAAAATCGTACATCTGCCACTTATCAGTTACTTTCAGATCCAAAGGAAACTCTAATCCCCTGAACTCCAAAAGGCGGTCCACATATCCAGAATGAGCTCAACCTGGACTATAGACAGATTACTGGCAGTTAGATAAAAGCCAGCATTCTCCAGGAATTGGTTCCCATCTGCCAAAATGAGTCATCTCCCTTACCTCTGGCAGAAGGGACAGATGGCTGGCTACTTGTGGCACCTATTCGTGTATCAAAGCTTATGCTGTCCTCCAGACTCCCTCTGTATCATAAGCACCTGTTAAACATTTCAAAGTCCGTGCATCCTAGCCCTTGCCACCCCTCCCCTCCCCTCCCCTCTCTCTGGCTCATGGGCTTCCATTCCCCAGCTACTCGTCCTTCTTATAATCAACTGTTTTTACTTCTCTGTGCTCCGGCTAGTCTATTCACTACCTATCTCCTAGCTCCATGGTCTCACTATCTCCACTATTCTCTCCTACTCTCTGCTTCCATAGCCCCGGGCATGTCAGGTCTGCTGGACATGTCCGGTCTACTTCTTTCTCCCTCTGCTCTGGATTCTTCCAGATGCCTCTAGATATTTTCTCTCTCTTATATCCAGTAGAATCCTTCCCCTTAGCCACACCAACAAAGCAGATCATTTTGGTAGTTATATGAGCATTGGAATGGCTTCACTTCTCTTCAGTATCTTCACCTGCATGAGGGAGACAATATGCTTGTAGAAGAATGACGTATATGGATCAGATGAGACAAAGTGTTTAAAGAGCTGTGGTTCACAGAAGCCACGCATTAGGGGATGCCTTCTCCATTGGAGGAAGATTAAAAAAAAAAAGAGAAGGATAATAAAGAAGCAGGCCAGAAGAGGAGGAAGAGAAGAGAGAGGTAGAGAAGAAAGGAAGAAAGGAAGAAGTGGTAGAGGAAGGAAGGGAGGGAGGGAGGGAAGGAGGGAGGGAGGGAGGGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATATTATGCCTGTGACAGAGTCTTATGCAGAGAAAGGGCAAGTCCTGGGTGTACTATTGTGTAAATACACTGGCCATCTCTCTCATCACCCACACCAAACCATGCTTGTACTCTGTTTCTTCACAAGAGCTTAATTTGATTCATCTTTTCCTGTCTTCTCCTCCCATCTCCTTTCTTTACTTTTAG
Seq C2 exon
AGTCTACCAAGACCTACGCAGACGTGGTCTTTCTTATTGACACCTCCCAGGGGACATCACAGGCTAGTTTCCAGTGGATGCAGAATTTCATCTCTAGAATTATTGGCATCCTGGAGGTCGGCCAGGACAAATACCAGATTGGGCTGGCTCAGTATAGCGATCAAGGTCACACTGAGTTTTTGTTCAATACCCACAAGACCCGGAATGAGATGGTCGCACACATCCATGAACTCTTGGTGTTCCAAGGTGGCTCCAGGAAGACTGGCCAAGGCCTTCGGTTTCTTCATCGGACTTTCTTCCAGGAGGCAGCAGGAAGCCGGCTCTTACAGGGTGTCCCTCAGTATGTGGTAGTCATTACTTCAGGGAAATCTGAGGACGAGGTCGGAGAGGTCGCACAGATCCTGAGGAAGAGAGGCGTGGACATCGTGTCTGTGGGCTTGCAGGACTTTGACAGGGCAGAACTGGAGGGGATAGGGCCTGTAGTGCTTGTGTCTGACCTGCAGGGAGAAGATAGAATCAGACAGCTAATGCTGGATGTGAATATGTTCATCCAGGGGAGTCCAAAGCCTCCACGGGTCATGACTGATGTTGCGAAGGACGCTGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572:ENSMUST00000121963:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.010 A=NA C2=0.010
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=90.9)
A:
NA
C2:
PF0009223=VWA=WD(100=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCAGTGATGAGGTCCAGGA
R:
CTGGTATTTGTCCTGGCCGAC
Band lengths:
358-1799
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