RnoINT0040220 @ rn6
Intron Retention
Gene
ENSRNOG00000031782 | Col6a4
Description
collagen, type VI, alpha 4 [Source:RGD Symbol;Acc:1564060]
Coordinates
chr8:114750002-114751478:-
Coord C1 exon
chr8:114751205-114751478
Coord A exon
chr8:114750560-114751204
Coord C2 exon
chr8:114750002-114750559
Length
645 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGA
5' ss Score
5.73
3' ss Seq
TGTGTTGCTCCTACCCCCAGATT
3' ss Score
10.56
Exon sequences
Seq C1 exon
TTAAGCAAAATGGCCCTGGTCTTCAGAAACACTGCCAGAACCAATGTTGCCCAATACCTCATCGTCATCACTGATGGTCAGTCTTCAGACCCAGTGGCTGATGCTGCGCAGGGACTGAGGGACACTGGAATCAATATCTATGCCATTGGAGTAAGAGATGCTAATACCACCGAGCTTGAGGAAATAGCGAACAACAGGGTATTTTTCACAGATGATTTTCACTTCTTGAAAAGCATCCACCAGGAAGTCGTTCGGGATATCTGCTCCTTCGAGA
Seq A exon
GTAAGAATTAAGACGTGATTGTATATTAATTATGCATGTAATTGGGTTTCACTATATTCTGTGTATGTATATATTTTGACCATACTCACCCCATCAGTCTCTCTTGTTACCCCTTCTTCTTTTTGCTGATCCCTCTTTTCTTTCTAACTGCTCCTTCTATTTTTGTGTTTTTTCTACCCCCTTTTCTTTTTTTCCACTCTCCCCCTGTTTGCAACCCAGGGAATTTCATGAAAGTTGCTATGTGAACACGGGTGAGAGGTTACTTACGGGAGCATGGGTACCTTGCCATGACCTCTACCGCTGATAGAGTATGATTTTTTTAAAAAAAATCTATTTAGTGCATCTTTAATTACTTGAATGGTCTTTATTCTCTTATGTAATTCACTGGCTGGTGAGTGACTTTTGAGCACAGAGTGACAGTGACCTGCCTAAACCAAGCTGGTCAAATTTTATTCTCTATCCCACAGCTGTGTCTTATTTTGAGACTAGTTTGTGCTGACTTGCAGAAAGCTTATCAACTATTTCTCATTCCCTTTAAGATTCTTTTTGTGCTGTGTATATACTACCGTTGGTGGTCGCTGGGGACTTGTAATCCGCTGGCTCCAGGTTTGATCAAATGTTCTCTTGTGTTGCTCCTACCCCCAG
Seq C2 exon
ATTGTAGGAGCCAGAAAGCTGACATCATCTTCTTGATTGATGGCTCAGAATCCATCTCTTCTGAAGACTTTGAAAAGATAAAGGACTTCGTGAAGAGGATGGTGAATCAGTCTAATATCGGGGCTGATAAAATTCAGATTGGCCTTCTGCAGTTCAGCTCCACTCCCCGGGAAGAATTCACGCTTAAGAACAATTACTCCTCAAAGGACGAGATGTGTAGAGCCATCTCGAATGTTACACAGATAAATAGTGGTACCGAGACTGGGAAAGCCTTGAATTTCACTCTGCCCTTTTTTGACATTTCACAAGGAGGGAGACCCGGAGTTCATCAGTATTTGATTGTGATCACCGACGGGGACTCCCATGATGATATAGTTTCCCCAGCCAAAGCCCTCAGGGACAGAAACATAATTATTTTTGCTATTGGGGTGGGAAAAATTCAAAGAGCCCAGCTCTTGGCGATTACTAATGACCAGGACAAAGTATACCACGAAGAAAATTTTGAGTCCCTGCAGAACCTGGAAAAGGAAATTCTTTATGAGGTCTGTACTTCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031782:ENSRNOT00000047563:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.011
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(50.0=90.2)
A:
NA
C2:
PF0009223=VWA=WD(100=93.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGACTGAGGGACACTGGAAT
R:
GTGAATTCTTCCCGGGGAGTG
Band lengths:
345-990
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]