RnoINT0040212 @ rn6
Intron Retention
Gene
ENSRNOG00000031782 | Col6a4
Description
collagen, type VI, alpha 4 [Source:RGD Symbol;Acc:1564060]
Coordinates
chr8:114755082-114760575:-
Coord C1 exon
chr8:114759988-114760575
Coord A exon
chr8:114755787-114759987
Coord C2 exon
chr8:114755082-114755786
Length
4201 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
CTGTGTCTTTCGGTTTTCAGAAT
3' ss Score
11.14
Exon sequences
Seq C1 exon
CCTGCACAGAAGCATTCCTGGCTGATATTGTGTTTTTAGTAGACAGCTCAACTAGCATTGGACTCCAGAACTTCCAGAAAGTAAAAAATTTCCTCCACTCCATTGTCTCGGGGCTTGACGTCAGAAGTGATCAGGTGCAAGTGGGGCTGGTCCAGTACAGTGACAACATCTATCCAGCCTTTCAGCTGAAGCAGTCCTCTCTAAAGAGCGTGGTCCTGGAACAGATCCGGAATCTGCCCTATAACATGGGGAGTACAAATACCGGAAGTGCCCTAGAGTTCATCAGGGCCAACTACTTGACCGAGATGAGTGGCAGCCGTGCCAAGGATGGGGTTCCTCAGATAGTTATTCTGGTGACAGATGGGGAGTCCAATGATGAGGTTCAGGATGCGGCTGACCAGCTGAAAAGAGACGGGGTCTTTGTGTATGTGGTAGGGATCAATATTCAAGATGTCCAAGAGTTGCAAAAGATAGCCAGCGAGCCATTTGAGGAGTTTCTCTTCACCACAGAAAACTTCAACATCTTGCAGGAGCTCTCAGGAAGCCTCAGTCAGGCTGTGTGTTCCACAGTGGAGAGAGAGATGAAAA
Seq A exon
GTAAGCCCTGTTCAATCTACCACTGACTCTACCAGTGAACCACAATGTAGCAATGGCCTTCCGAAGGGGAAGGAAGGTCTACCATCATGGGAGCATCTGGGGATGTTTCCTAGAGCAGAGGAAGTCTGAGTTGGCCTTGAAGGATGAGTAGAGAAGCTCGTAGGTAGAAAAGAAGGGAGAAGACTTGTTGTTGTGTTGTTTAGAAGAAACAGCCGGGGCTTTGGAGTGCACAAGTCATACTTTTAAAATCTTGCATATGCAATTTACTCTCAGATCCAAAAGAAACTCTAATTCCCCAGACTCAAAAAGGCACCTCCATATATCCAGAATGAGCTCAACCGGGACTGTAGGAAGATCACTGGCAGTTAGATAAAAGCCAGCATTCTCCAGGACCTTGTGAAACTGGTCTCCATCTGCCAAAATGAGTCATTTCCTTTACCTCTGGCAGAAGGGACAGACGGCTGGCTACTTGTGGCGCCTATTAGTGTATCAGAGCTTATGCTGGCCTTCAGACTCCCTCTGTATCACAAGCACCTGTTACACATTTCAAAGTCCATGTATCCCAGCCCTTGTCACCCCTCCTCTCCCCTACACTCTCTCTGGCTCATGGGCTTCCATTCCCCAGTGCTCATCCTTCTTAGAATCAACTATTCCTACTACTCTGCTGTGGCTAGTCTTGCACTCTATTGTCTATCTATCCCCCAGCTCCACGGTCTCACCATCTCCACTATTCTCTCCCACTCTCTTGTTTCCATAGCCCTGGCCTTGTCAGACGTGTCCGGTCTACTTCTTTCTCCCTCTGCTCTGGATTCTTCCAGATGCCTCTAGATATTCTCTCTCTTATATCCAATAAAACCCTTCCCCTCCGCCGCACCACAAAGCAGGTCATTTTGGTCGTTATGTGAACCTTGAAGTAGCTTCACTTCACCTCAGTGTCTTCACCTGCATGATGGAGATGATATGGTTGTAGCAGAATCACGTATAAGGATCAGATGAGACGAAGTGTATAAAGAGCCGTGACTCACAGAAGCCACACAGTAGGGGCTTGTTTCTTGCCTTCTCCATTGGAGGGAAGATTTAAAAAAAAAAAAAAAGAAGCAGGTAGTAAAGAAACAGGCCAGAAGAGGAGGAGGAAGAGAAGAGGGAGGTAGAGAAGGAGGAAGTGTAGAGGAAGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAATATGCCTGTGTTGGAGTTCTATGCAGAGGAGGGGCAAGTCCTGGGTGCACACTATTGTATAAATACACTGCCCGTCTCTCTTGTAGCCCATACCAAACCATGCTTGTACTCCATTTCTTTACAAGAACTCAAGTTGATTCACCTTTTCCTGTCTTCTCCTCCCACCTCCTTCCTTTTCTTTAGAGCCTACCGAGACCTACGCAGACGTGGTCTTTCTTATTGACTCATCCCAGGGGACATCCCAGGCCAGTTTCCGGTGGATGCGGCATTTCATCGCTAGAATTATTGACATGCTGGAGGTTGGCAAGGACAACTACCGGATTGGGCTGGCTCAGTATAGCGACCAAGGTCACACTGAGTTTTTGTTCAATACCCACAAGACCCAGAATGAGATGGTCGCGCACATCTATGAGCACTTGGTGCTCCAAGGTGGCTCCAGGAAGACAGGTCAAGGCCTTCGGTTTCTTCATCGGACTTTCTTCCAGGAGGCAGCAGGAAGCCGGTTCTTACAGGGTGTCCCTCAGTATGTGGTAGTCGTTACCTCAGGCAAATCTGAGGACGAGGTCCGAGAGCCTGCACAGATCCTGAGGAACAGAGGCGTGGTCATCATGTCCGTGGGCTTGCAGGACTTTGACAAGGCAGAAATGGAGGGGATAGGGCCTGTAGTGCTGGTGTCTGACCTGCAGGGAGAAGATGGAGTCAGTCAGCTAATACAGGATGTGATTATGTCGATCCAGGGGAGTTCACAGCCTCCACAGGTTTTGGTCAAGTTTGCGAAGGAAGTTGTAGAAGGTAAGTAAACCTCAGTCCTTGGCTATGTGAGTCACCAGGAAGTCACAGGGCATGAAGAAAATGTAGGGGTCTGGGGGTGTAGTTCAATCGATAGAATGCTTGCCTAGCATGCATGAAGGCTTGGGTTTGGTGCCTGGTACCACACATAAACTGGTACAACCAAGCATGCTTGTAACCTCAGCACTCTAGGTGTAGAGAGACAGGAGGATCTGAAGTTCAAAGTCAGCTTCGTTAGTTACTGTGTTTGATGCCAGCCTCTCTCCATGAAGTCATGTTATTTACTTTATTTTTCCTAAGGAGAGAAGAAGTGGAGAGGAGGAGGAGGAGGAGGAGGAGGAGAGGAGGAGGAGGAGGAGGAGGAGGAGAGGAGGAGGTGGTGGTGGAAATAGTTGGGAAGGCATTCTGCATCCCTCAGTATGGAGGGACTCGTCCCTGTAGACAGGGAGGAGAAAGAGGACTCGGGGAATGCCTGTTAGATATCTTGAAGGTATGCCCGCAGTCCACCACTAATACGCTGCTAATATCTCTGGTTGGAAAAGATTTCTCCTCACATGTCGTCGGTTGCTTGTAAAGTCCAAGTGGTGGCTATCTTGTTGGTTCTTACCTGTGGCCTATTAGCAGGTTCTGAGGCCTCAGCTGGGGTTGTCTGCTTCTTGAGCGGATCCAGCTAGCTCTGAGCAAATTCTCCCTTGTGGGCAATTGCAGAGACACAGAGAAAAATCAACTGTATAAGGTTTTCATATCTCTCCAGGCACGCTACTGGGCTATTAGTGAGAAGCAGTCAACGTACCGCAGTCATCATCTGTGGGAAAAGTATATTTTTTCCACGGGCCAATGAGAACACGGAGCCGGAATATTTCTGAATAAACCCCATGCTAGCAATATGTTTTTTAGACAGACCATCAACCTTTCATTTTAGTTTACGTGAATGGGTGTTTTGCCTGCATATGTGTCTGTGTACCATGTGTGTGCCTGGAGCTTGTGGAGGCCAACAGAGGGCGTTGGATTGGATGGAGTTGCAAAAAGCTGAGGGCCACCCATGGGCTCTGGGACTTAGATTCTTTGGAAGAGTAGCGAATTCTTTCAACTGCTGGGCCATCCCTCCTCCCTCTTGTTTATTATTTTTATTCATATGTGTATGTACCTGTGTGAGTTTGTGCGTACCACATACATGAAGGAGTCCCTAGAGTTCCAGGTGGCTGTGAGCTGTCATGGAGATGCCTGGAACTGAGCGGAGCTCAGTTCAAGAGCAGGAAATACTCTTAAGCACTGAGCCACGTCTTCAGCCTCTCAGTCAATTAGTCAATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCAACGAAGTCTCACTAGATAGACCAAGATGACCTTGAACTTGTTATTCTCTGCCTTGGCCTTCCAAGGGCTGGGATTATAGTATAGGTATGTCTCACTGTCTGTCTAGTTAACCTGATGTTCAGGGAAAGATTTTTGCACAATTTGCAGACCTTCATGAAGGGGGCAAAAGTGATTAAACAAAGTGTGTTTCAGACCCATAGAGAGGATTTTTTTAAGATTTATTTATTTAATTGCATATGAATACACTATAGCTATCTTCAGGCACACCAGAAGAGGGCATCAGATCCCATAACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCACTGAGCCATCTCTCCAGCCCTCATAGAGAGGATTTTGACTCATAGTCTTCTTGAAGGTAGAAAAATGAAGGAAAAAGCCAGCCAATATCCCGAGCTTCTAAGGTTGTTAGACAAAATGGAAGGTGGTCTTGAGTGGTTTTCCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTTTGGTGAGATTTTTTGGGATATACATGTACCTCTTGATGCATTTTGATTACAATGTAAAAAAAAGACTTTCTCTAAATTCTAAAGCACACAATTAGAAGTTAGTATACTGTAACTTAAAACCTTAGACACATTATTATGACAGACGTCCAAGCTTTATATACGAGTGTTTCCTTATTCCTCTACTCTCAGGCTGAGACCCTCTGTGTCTTTCGGTTTTCAG
Seq C2 exon
AATGTCTGGCTCCCATTCCAACTGACCTCGTGTTCCTCGTTGAGGAATTTACCAGTGCCGGGCAACCCAATTTTCAGCAAGTCATCAAGTTATTGAAGACCACTGTCCACTCTCTCAACATCCACCCTGATATCGTGAGGGTCAGCTTGGTCTTTTACAGTGAGAAACCACAGCTGAAGTTTTCTCTGAATACATTTCAAAATGCTGCCCAGGTCTTAACCAGTTTGGACCAGTTAACCTTCAGAGCAAGACGAGGAAGGACGAAGGCAGGGGCTGCTTTGGATTTCCTGAGGAAAGAAGTTTTTCTTCCGGAGAAGGGCAGCCGGTCCATTTGGGGTGTACAGCAGATAGCTGTGATCATTATGGAAAGTCCATCTCTAGACAATGTGTCTACACCGGCTTCCCACCTCCGCAGGACCGGGGTCACCATCTATGCAGTGGGCATCCAGTCTGCCTCTGAGAGTAAGGACCTGGAGAAGATTGCCACATACCCTCCTGGGAAGCACACCATTCACCTAGAGTCCTTTCTGCAGCTCGATGTTGTGAGAAAAATACTTAATAAGAAGCTCTGTCCTGAGACTTTGGGCAAAATGCCTCCTGTGGGCAGCATGCCTCCTGGGGCCGAAATGCCTCCTGGGGCCGAAATGCCTCCTGGGGGCAAAATGCCTCCTCTGACGGGTTGTACTCCACAGAGCATGCAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031782:ENSRNOT00000047563:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=0.178
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=89.8)
A:
NA
C2:
PF0009223=VWA=WD(100=75.4)
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
Zebrafish
(danRer10)
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]