DreINT0050262 @ danRer10
Intron Retention
Gene
ENSDARG00000079752 | col6a6
Description
collagen, type VI, alpha 6 [Source:ZFIN;Acc:ZDB-GENE-041111-303]
Coordinates
chr16:36754310-36755804:+
Coord C1 exon
chr16:36754310-36754406
Coord A exon
chr16:36754407-36755138
Coord C2 exon
chr16:36755139-36755804
Length
732 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
AACATCTTTTCACATCCAAGATC
3' ss Score
3.24
Exon sequences
Seq C1 exon
GCAGATGAGAGCCAGAGTTTTATCCTGACTGTTCTGGGTAGAGTGCAAGACCAGAATGCTACTCTTAGTAAGATCCAGAGTTGTGTTATTTGCTATG
Seq A exon
GTAAGTTTTTTTTTCTCCTGCTTGCACCCAAGGATTAATGAAATGACATTAAGAGGAAAAAAAAAAAGACATTTCAAGGGGATTTAGGCATTTATATTATATTATATTATGTTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTACATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTACATTATATTATATTATTTTATATTATATTATATTATATTATATTATGTTATATTATTTTATATTATATTATATTATATTATATTACATTATATTATATTATTTTATATTATATTATATTAAATTATATTATATTATATTATATTATATTATATTATATTATAATACATTTTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTTTGCCAAATTTAAAGTCAGTTTTTTCAGTATTACTTTTTTAAAGTCTCATATTACATATATTTTCAAACAGTTTTTTTATGATGTATAAATCTCAATCACAGTAATTAAGGAATAATTGAAAAAAATGTACACCCGAGGTTTGGTATTTTTTATATACTTTTGTTTTTGTATTGTACTTTTAATAAACTGTTTCTCCAGAACTTTTTCCACCTATTTATTGTATGATAACATCTTTTCACATCCAAG
Seq C2 exon
ATCCCTGCAGACCAGCTAGAGAATGTGAGGGCACCAACCTGCCATCTGCACCTCAGGAGCTGGACATGGACTTTGTGATGGTTGTGGACGGGTCCCGTAGCATCCTGGCTGACGAGTTCAAGGGTGTCAAGGAGGTGCTCGGCGGTGTGCTCGATCAAATTGTTGTGAGCAGTCAACCCACCAGGGCTGACAGACAGGCCAGAGTGGCTCTCTACCAGCAGACGTCTACCTATAGTGACCCCCAGCCTGCACACGAGATATTCAGCTTACGTGAGTTCTCTGATCGCAATCTAATGAAGACAAGCATCATCCAAAAACTAAAGCAAACCGGAGGATCTCATGAACTGGGTTCTACTTTGGAGTTTGCTTTCAAGAAGTGTTTCAACGCAGTTCCAGAAAGTCGCAAGAACAAGATGCTGCTGGCCATCATTGGGGAGGAGACAGCGTTACAGGAGAAAAAACGTCTGGACTCTTTCTCCAGGTTGGCGAAGTGTAGCGGCATTGTTCTTTTCACCTTGACAGTGGGAGACTCCATCGCCTCTAGTCAGGTGGAGGAGCTTGCCAGCTATCCTTTAGAACAGCACATCATTCACCTGGGCCACTTGAAACATGGAGAACAGGAGTACACACAACGCTTCATGAGGACTTTCTTCCATATACTGAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079752:ENSDART00000109703:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.032
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(12.4=66.7)
A:
NA
C2:
PF0009223=VWA=WD(100=82.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGTAGAGTGCAAGACCAGA
R:
TTGCGATCAGAGAACTCACGT
Band lengths:
352-1084
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]