GgaINT0041675 @ galGal3
Intron Retention
Gene
ENSGALG00000006626 | PDE6C
Description
NA
Coordinates
chr6:21470236-21471298:-
Coord C1 exon
chr6:21471149-21471298
Coord A exon
chr6:21470380-21471148
Coord C2 exon
chr6:21470236-21470379
Length
769 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
TTTGCTTTGTTTTGTTCCAGACT
3' ss Score
9.51
Exon sequences
Seq C1 exon
AAAGGACCTGTGGATGAGACTGGATGGGTTATCAAAAATGTCCTTTCATTGCCTATTGTCAACAAAAAAGAAGAAATTGTGGGAGTTGCAACATTTTACAACAGGAAAGATGGAAAACCTTTTGATGAATATGATGAACAGATAATTGAA
Seq A exon
GTAAGTTTAATAGGATTACAGACCCTAAGGAGCCATATGATGCTAAATTAACAATTTTTAGCAGGCTATATTAACATCTGACCAAAAGATTACCTTCCTCACTATAGTTTCTTAAGAATGAGAGATTTTTTTTCTCCGTTTATAAAACTGAAAATTTATGAGATCATTTACATTCCAGTAATGAACCAAAGTCAGATATTTTTAAGTCATTTGACTCTTTAATGATGGTCAACGTTCATAATTAATGTGAGTGGGTTAAAAATGGGATGGAATGGAACAGTTCAGATTCAAGGAACTTCTGAAGGTCTTCTAGTCAAACTGCCTGACCACTGCAGGGCTAACCAAAAGTTAAAGCATAATATTAAGGACAATATCTAAATGCCAAATATTAGCAGGCATGGCATGCTGCTTACCAATGAACATGCCTGCAATCATCAACTCTAAGGGAGACCATGTACTTTGGCAAGATATGATATTACACATTGTATTCAAGTCCCCAAGCTAACCTAAACTTTATAAGCCTCAAACTCCTGTATATAAGATGGGAATATGGGCCTGTAGTTACACAGTTTGAAACAAACAATGTCCTTAAAAGCTGTGAGGGTCAAATGGCACCTGTTGATGGGAAGGTGAAGTCTTCTAACAGGAAGAATCGAGTGTTGATTTTCAAAGAGCATGATCAGAATGTAAATTTTAAGAGTTAAGTTTAAATTGGCAGTTCAATGTTACTGTCATACTGTCACCTAAACTTTGCTTTGTTTTGTTCCAG
Seq C2 exon
ACTCTTACACAGTTCCTGGGGTGGTCTGTTTTAAATACTGACACTTATGATAAAATGAATAAGCTTGAAAATAGAAAAGACATTGCTCAGGAAATGCTTATGTATCAGACAAAGGCTACTCCTACTGAAGTTGAATCTATACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006626:ENSGALT00000010702:9
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=0.000
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(27.5=100)
A:
NA
C2:
PF0159021=GAF=PD(5.1=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGACCTGTGGATGAGACTGG
R:
AGATTCAACTTCAGTAGGAGTAGCC
Band lengths:
286-1055
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]