DreINT0050261 @ danRer10
Intron Retention
Gene
ENSDARG00000079752 | col6a6
Description
collagen, type VI, alpha 6 [Source:ZFIN;Acc:ZDB-GENE-041111-303]
Coordinates
chr16:36753132-36754406:+
Coord C1 exon
chr16:36753132-36753625
Coord A exon
chr16:36753626-36754309
Coord C2 exon
chr16:36754310-36754406
Length
684 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAG
5' ss Score
8.27
3' ss Seq
ATATGTTGTACTGTATGCAGGCA
3' ss Score
5.27
Exon sequences
Seq C1 exon
ACAACATAAAATGTCCGGCATACCCCACTGATCTTGTGATTGGCATGGACATGTCTGAAGATGTGACCCCTCAAGGCTTTGAGCGCATGCGTTCTGTGGTCCTCAGACTGCTGGACAACATGAAAATTGCAGAGAGTAGCTGCCCGACAGGGGCTCGAGTGGCTCTGGTGTCCTACAGCTCATTCACCAAATACCTGATCCGCTTTAACGACTACCACCGCAAGAAGCAGCTTATCGATGCCGTCAACAACATCGCCCTGGAACGCACTTCAAATCGCCGCAACATTGGCGCTGCCATGCGGTTTGTGGGCAGAAATGTTCTGAAGCGAGTGCGAAAAGGCATCCTGATGAGGAAGGTTGCCATTTTCCTCACTGCTGGAGAATCTCAAGATTCGATATCTCTCACCACTGCCATTCTAGAGTACAAAGCCCTGAATATTAAACTTGGGGTCATTGCTCTGAGGAATGTCCCTGCTATCAGGAGAGCTTTTGAG
Seq A exon
GTAAAGATGAGTGCCTCATAAACAAAATGTTTAAAAATAGCTGATTGATTTAAAAGTGGTTAACTCTTTAAATTGGTTAACTTTGTATGCGTTTTTAACTCCAAGGTGACCAGTTGTTTGAACTACTATAATTCACTAGTATTATTCAAACTAAAAACATCTCATCCACAATGACCTGAGCACTTAAAAAAACACTCCCCCCCCTCCTTAGCTCTCCCTGAGCACTAACTGTTACTTTTTATAATTAGCACTTCTTGCGTGTATTGCCTCTTCTTGTTAAATCACTGAATGTCTCCTCATTTGAAAGTCGCCTTGGATAAAAGCATCTGTTAAATGCAACATAGGCTCATTGTGAAAACATAGCCCTGTATACATTTCTGGAGAACGCAAATTAGGGAGCCAAGAGTACGTTTGGCTGTGTTTCGTTTTTTAAACGAGCGTTACGTGGCAGTATGATGCCATTCTTTTTTGGGCTTACCAGCTGACCGCTTCAATTTGGAAGGCTTTTCCGCTGTTACCAGTTTGTCCAGTAGCGTTTTCAGAACGAGCCTGGGTTGGTTTAATGGCTAAATGTGAATTGTAAAATCAAGGTGTGTGTGTGCCTAACACAAGAAGCTTTAATACTTTTAACAGCATGTAGACATACTCATTCTCTATGCATGGCATATGTTGTACTGTATGCAG
Seq C2 exon
GCAGATGAGAGCCAGAGTTTTATCCTGACTGTTCTGGGTAGAGTGCAAGACCAGAATGCTACTCTTAGTAAGATCCAGAGTTGTGTTATTTGCTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079752:ENSDART00000109703:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.006 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(87.0=93.3)
A:
NA
C2:
PF0009223=VWA=PD(12.4=66.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTTAACGACTACCACCGCA
R:
TGGTCTTGCACTCTACCCAGA
Band lengths:
346-1030
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]