DreINT0050232 @ danRer10
Intron Retention
Gene
ENSDARG00000077139 | col6a3
Description
collagen, type VI, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-070501-8]
Coordinates
chr9:24105489-24107686:-
Coord C1 exon
chr9:24107633-24107686
Coord A exon
chr9:24105552-24107632
Coord C2 exon
chr9:24105489-24105551
Length
2081 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGT
5' ss Score
8.94
3' ss Seq
TGTTTGTTCTTCTACCACAGTGG
3' ss Score
7.69
Exon sequences
Seq C1 exon
TGGCTGAGCATAGTTCAAGTGCTGTTCTCCCGCCAGCACCAGCTCCAGCTCCAG
Seq A exon
GTCAGTGCACTATGACCATAATTTGAAAAAGGGATCTTTAATTAGAGTTTGATAAAATTTTGCATTTTAATTTCATTTTTTCAGCTGTCTGAGCTGTATGATCTCTAGGGATGGGTTGACTTAACAGTTTTTTATATTACTGATATGATATGGAAGCAATGTATTAACTTTATACAGTTGAAGTCATATTTAGTAATCCCCCTTTGATTTTTTTTATTTCTTTTTTAAATATTTGCCAAATGATGGGGGGCTAATAATTCTGATTTCAACTGTATTTTTATTCTTTGATTTTTATTCATGTTATTACGTTTTGACAGATGGTATATTTAGATGGATAGATAGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAAAAATGAAGGCTAAAAGAAACATGGAAAAATCTGTGCTGGAAACAATGATTTCTGCATTGTGTTCTGATGTGGTATTCAGCATTTAGTATTCATAGCAGAGCAATGAGGTCATAATCTTTTTTAGATGGAAACAGGGAACCCCATTTCCTTCTATGCAGTTGGACTTTTAACATGACTGCATCTACAAATAATAAACTAACCAAAGGAAAATGTTGACCAACACATCATTTTACTTACAGCAATAACCCACTAACAAAGAGCAATACTTAAAATGAATGAGGGGGAAAAAACACACAAAAGGCATGTTTACTCAGGAGGGGTTAGGAAGCAGACATTTGTGAAATGTGGCCCCTGCATAGACACTGTTCATGGGTCTGACATCATACTTAATTACCAGCAGACTGCAAGTGTATAACACAGCTATCAAATGAACTTCAAACAAAGCATAAAGTTTAACTGTCTTTGTGAACAAGGTCACTGCTTTTTTTTTTTTTTTCTGGTGAAATAGTACAAAAGTGTATGCCCTTAGAAACTTCAGTCCTATTACAATGCAAAAATCAATGACTAAAGAATTCAACCTTCTCTATTTGTGTGAAACACTGTGTTTTAGTAGCCTCTGCAAGTATAACATGCAAGAAGAAATTATTGAAAATGTCACATACTGTGGTTTGTATGTTCTTTTAATCTGGCTAACCCCTTTTTTTAAAATTCCTAATCCCCTTTAAATGAGCTATATAATCACTTATAGTTTCCTGACTGTTCGTTTAACTGGAAACACTAACTGTCTTTGTCCTCTTTCATGATAAACCCTCTTTTGTATGTTTGCATGTTTCAGTTAACACTCTTTTGGAGCCATGCTCACTTGACTTTGACACTGGACTACCATGCAAAGATTACCAAGCTAAGTGGTACTTTGACAGAAAGAATGGATTCTGTACACAGTTCTGGTATGGAGGTTGTGGAGGAAATGACAATAGGTTTGAAACTGAGTCTGATTGCCTGAAACGCTGCATGAAGACAGGTATGTGCACGCTTTGATCCCTTGGTCTGGGGTCTTTATGAATGAATTAAATCACAATGTAAATGCAGTAGTTGCAGTACTTGTGATATTGTCTTAATCTCTTAAATCCAGAAATATGATGAAACTAGGTAGAGTGATGTAGTAAATTAATCACTATGTTTAAATGTGCACCAGTAATTAGAGTCAGTAAATATGACTTAATTATTGTGAGATATGTTTACATGACACATAAATCCTCTTTATTGCAATTTATTAACCTCTTTACAAGCCAATATTGTATTGTTCCGATTATTTGCTACATGTGCAAAGGTTTCATTGCATTATTGAAAAAAAAAATGTTATAATTAAATAACAATCAGTGAATGTAAGCATAGTCATTGTATTATTACCTCAGTAATTCTGCAGCACACAGCTATGGCATTAGTAGCCTGGAGATTGCCCCTCTTTAATAGGAGGAGCAACAAATGAAAGACATTCAAATTCTTGAAAAATGAATTCCACTTGTTTGTTCTTCTACCACAG
Seq C2 exon
TGGCTGAGCAAAGAGCAGCTGACGAGCATATCAAAGCTGTTTTGCCGCCAGCACCAGCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077139:ENSDART00000138754:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.851 A=NA C2=0.370
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
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]