GgaINT0126126 @ galGal3
Intron Retention
Gene
ENSGALG00000001910 | SNAPC4
Description
NA
Coordinates
chr17:8585948-8586498:+
Coord C1 exon
chr17:8585948-8586020
Coord A exon
chr17:8586021-8586333
Coord C2 exon
chr17:8586334-8586498
Length
313 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
TTTCTCTCTCTCTCTTTTAGTTT
3' ss Score
13.36
Exon sequences
Seq C1 exon
CCAACTTCCAGAAAGTGACTTGTTAGGAGGCAGATTTGATGAGCATGACTGGGAGAAGATTGCAAACGTTCAT
Seq A exon
GTGAGTTGGTAGATCAGCTGTTGTATTCTAACATCTGTCCCCTTTCTCTTGAGAATTGCCTGACCTGCTGTCATTTCCATCCACTGATCCCCTCATGCCCTTCTGTAAGTTGACTGTTGTGTGATCTCGATATGGTAAGCATATAAGCACTTAAAATTGGATATCCCTGGTTAAATCTGATGCTTTACTTCTGACAAAATTAGCACCAAGACACGCGTGGAACACAAACTGTATTACACATAGCTGGGCCAAACATCTGGGCAGAAATGAATGCTGACACAAGACAGAATAGATTTCTCTCTCTCTCTTTTAG
Seq C2 exon
TTTGATGGACGGCGCAGTTCAGAAGAGCTGAAGAAGTTTTGGCAAAACTGGGAGCATCCAAACATCAACAAGAATGAATGGACAGAGGAGGAAACAGAGAGGCTGAAGGATATTGCAGCTAAACGTGGTTATTTGGACTGGCAGACCATAGCCCAGGAATTGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001910:ENSGALT00000002951:9
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=0.145
Domain overlap (PFAM):
C1:
PF139211=Myb_DNA-bind_6=PU(0.1=0.0)
A:
NA
C2:
PF139211=Myb_DNA-bind_6=PU(45.9=50.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCAGAAAGTGACTTGTTAGGAGG
R:
CCAATTCCTGGGCTATGGTCTG
Band lengths:
230-543
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]