RnoINT0040201 @ rn6
Intron Retention
Gene
ENSRNOG00000031782 | Col6a4
Description
collagen, type VI, alpha 4 [Source:RGD Symbol;Acc:1564060]
Coordinates
chr8:114759988-114763553:-
Coord C1 exon
chr8:114762951-114763553
Coord A exon
chr8:114760576-114762950
Coord C2 exon
chr8:114759988-114760575
Length
2375 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
TGTTTACTCCTCTCTTGCAGCCT
3' ss Score
10.05
Exon sequences
Seq C1 exon
TCTGCAGGGAGGCCTCTGTGGGAGACATCGTGTTTCTGGTCCACACCAACATCGACCCCCAGCATGCCCAGAGTGTGCGGAACTTCTTGTATATATTGGCAAACAGTTTACAAGTCGGCGGAGATAACATCCGTGTGAGTCTGGCCCTGTACGGTGATACACCCACCACTGAGTTCCTGCTTTCGGCCTATCCCCGCAAAGGTGATGTGTTGAAGCACATCCGTGGACTTCAGTTTAAGCCCGGAGGCAACAGGATGGGCCAGTCCCTGCAGTTCATCCTAGAGCATCACTTCCCGGAAGGAGCCGGGAGCCGGGCAAGCCAAGGGGTGCCTCAGGTGGCCCTGGTGATGAGCACTGGTGTAGCTGAGGACCACTTTCGTGAACCTGCCGAAGCTCTCAAGAGAGAGGGAATCTTGCTATACGCCATTGGAGTCAAAGACGCAGCTCAGGCCGAACTCAGGGAGATTGCGAGTAGTCCCAAGGATAACTTCACCTTTTTTGTTCCTAACTTCTCTGGCTTGCCTGGCCTCGCCCAGAAGCTGCGGCCAGAGCTTTGCACTACACTAGCAAAGGTAGTGCAACATACTGAGCAGGGATCTCCAG
Seq A exon
GTAACTTCTTCTTTCTCATCTGGACATTAAAGAACTCCAAACTTTGTCTTTCTCATACCCCTTTACTATGCTCTTGTTTATACGTGTGTAAATTCAACTCAGAGGTTACAAATTCACGCATCAAGATATATCTGTTTCCCCAACCATTGGCCACGACTCTCACATCCCGGGGGCCTGTGGCGGTGCCATACACGGAACCAGTGTAAACCCAGTTTTGAAGGAAGGATTATCTGTTCCTAGAATAGCATAATTTTTCATGGGTTTTCCTGCCCATCTCGCATGGCCAAGGGGCAGGAGGTGAGTGGACCAGGAGGCCCCCAGGGCTTTTGTTTGCCTCATGGTCAGTATGCTGGTTAAGAGGACACATTTTAGAGAGAAGAAAGACCCCAGCTTAGATCCTGTCTCTCACTTCTGGTGCCATCTTGGACAAGCCATTTAACCTCTCAGAATCTGAAATTTCTCCCTAGGACGATAACCCCTGGATCAGAGAGTCAGAAGCATTAAACAAGATTGCATAGTTACAAAGCTTGGCACAATGGCTCCCCAACTAGGGTTACCCACATGTTTTGCCTGTTGGCGCCTGTGAGAGCATATGCCTGTCTTCCACTTCCTTCTGCCCTTGATAGGACCCAAATGGATGAAAATAGTTCATAAGTTGGTTACTCAGCCTTATTGGAAAACACTCAACTTTGTTTTTCAAAATTCTCTTGACGGATTCATTTTAGACTTCCTAAGGCATAAAACTTCAAGTTGAGAAAGAGATGACTGTGTGTGGTCCCGGTCGAACTCCACAAGAGGACAGCCCCCTCCCCATTGTCTCATTATTCTGATATTTCCTTTTAAAAGCATATGACTCGGAAGGTGTGCTAAAACCCGACAATGTGTGGCATTGAACAGAGATCATATACTTTAAAAATAGCACCTCAAGGTTAACAAAGATGTCATATGTATGTAGTCATAACTACCACCCGCTTGTAGAGCACAGCAGTAGTTCTTAACCATCCTAAGGCCACAACCTTTTTTTTTTTTTTTTTTTTCTTTTTTTCGGAGCTGGGGACCGAACCCAGGGCCTTATGGTTGCTAGGCAAGCGCTCTATCACTGAGCTAAATCCCCAACCCCGGCCACAACCTTTTAATACACTTCCTCATGTTGTGGTGACCCCCCCCCAACCACAAAATTATTTTCATTTCTACATAACTGTAATTTTGCTACTGTTATAAGTCATAGTATAAATATCCCTGTTTTTCAGTGGTCTTATTAGACCCCAGTGAGAGGGTTGCTTGACTCCTTGAAGGGGTTGCGACCCCCAGGTTAAGAACCATGGCTCTATTTCAAGCCTTACTTACATCTCTCATTAGGATGTTCAGTGGTCTCCGATTTCTAAATAAGCAGGATGGTTAGTATGACTACTTTTGCGTTTCTCAGATACGGAAACTGAGGTTTTGGCACTCTTAAGTATGTGGTACAGCTAAGGAGTTGTTTCCCAGAACTGCTAGACCTCTTGTCTAGGGCAGGTGTGTTAGAGTGTTTCCAGAAGCAGAGCCCATGGCAAAAGCTGGAAGGACATAATTTAATGTGATTTCCCATAAGGCTGTGCTAGAGATGCAGAGGAAGGGAGGAACGGCGTGAACTCTGCCAAAAGGTCCTCAAAGCCGGTGTTGTCCTGACCCTTTGTGGGAACTCAACAGCACAAGTTTTGTGGGAACTTAAGAGCAGATTTTATGTCTCGGGGTTGTCTTGACCCTGAATCTAGACCCAACAAGAATATGGCTTTTGTAAAATTGAGAAAAAGATAGTAGGGGTGTGTGTGTGGGGGGGAGTCCTCCAAAGATCAATGCTTGGAAATGGTCAGAAGGAGTCAGTAGGACCCAGGCAGAGTTGCATGTCTGATATAGTAGATGGTTTTCAAACCACCCAGGAGTTGGGAGGTATTTCGGTGGCAGGAGAAGAAAAGTCTCAAAGAGTGACAGATCACAGGGCCGCTAAGTGCTAGACCGGCAATGAGACTTACTGTAGAGAATGGGACATGTCCTAGCTCTTTGACCTGTCAGGGCCAGCATGTGCCTGGAGAGGAGATGTTCATCCCAAGAGGGGAGACAGGACATAAGACCATAACTCTTTCAGTATGCTGTTAAAATTGCAGAAGACTTACCTTCTTGATGTGAGTCTGGGGGGATTTTAAGGCTGGCAGCAGCAGCAGCAGCAGCAGGAGGGTGGGCCTGAAGCCTTTGAAGATGAAGAGGGGAGGGGAGGAGAGGACACACTCCTGCACACCATCTTTCTCCCTTCCTCCGGCTCAGCATTGTGCTTTACCACCTCTAGGTATTTAGAACGAAGCCTCTGAGACTCCCTTCTGTTTACTCCTCTCTTGCAG
Seq C2 exon
CCTGCACAGAAGCATTCCTGGCTGATATTGTGTTTTTAGTAGACAGCTCAACTAGCATTGGACTCCAGAACTTCCAGAAAGTAAAAAATTTCCTCCACTCCATTGTCTCGGGGCTTGACGTCAGAAGTGATCAGGTGCAAGTGGGGCTGGTCCAGTACAGTGACAACATCTATCCAGCCTTTCAGCTGAAGCAGTCCTCTCTAAAGAGCGTGGTCCTGGAACAGATCCGGAATCTGCCCTATAACATGGGGAGTACAAATACCGGAAGTGCCCTAGAGTTCATCAGGGCCAACTACTTGACCGAGATGAGTGGCAGCCGTGCCAAGGATGGGGTTCCTCAGATAGTTATTCTGGTGACAGATGGGGAGTCCAATGATGAGGTTCAGGATGCGGCTGACCAGCTGAAAAGAGACGGGGTCTTTGTGTATGTGGTAGGGATCAATATTCAAGATGTCCAAGAGTTGCAAAAGATAGCCAGCGAGCCATTTGAGGAGTTTCTCTTCACCACAGAAAACTTCAACATCTTGCAGGAGCTCTCAGGAAGCCTCAGTCAGGCTGTGTGTTCCACAGTGGAGAGAGAGATGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031782:ENSRNOT00000047563:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.005 A=NA C2=0.015
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=87.1)
A:
NA
C2:
PF0009223=VWA=WD(100=89.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
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]