GgaINT0126127 @ galGal3
Intron Retention
Gene
ENSGALG00000001910 | SNAPC4
Description
NA
Coordinates
chr17:8586334-8586868:+
Coord C1 exon
chr17:8586334-8586498
Coord A exon
chr17:8586499-8586720
Coord C2 exon
chr17:8586721-8586868
Length
222 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGT
5' ss Score
9.65
3' ss Seq
TATGTTTTCTTTCCACGAAGACA
3' ss Score
5.45
Exon sequences
Seq C1 exon
TTTGATGGACGGCGCAGTTCAGAAGAGCTGAAGAAGTTTTGGCAAAACTGGGAGCATCCAAACATCAACAAGAATGAATGGACAGAGGAGGAAACAGAGAGGCTGAAGGATATTGCAGCTAAACGTGGTTATTTGGACTGGCAGACCATAGCCCAGGAATTGGGG
Seq A exon
GTAAGTAGTTCTGAGGCCAGAAACATGAGGTGGGAAGTCGGGTAATTCTGATGGTACCTCATCAAAAGTTTTGGAAAACAAAGTTAATATTAATTCATTGTTAATTAATAGCTTTGTGAGGAGTATTCAGGAACAGAACCAAACAATTGAAACTTTTGCCCTCTTGATTCTGTCCTCCTCAATATCCAACTGTCTAAGCAGCTATGTTTTCTTTCCACGAAG
Seq C2 exon
ACAAACAGGACAGCTTTTCAGTGCTTGCAGAAGTACCAAACCTATAACAAAGACTTGAAAAGGAAAGAATGGACCAGAGATGAAGATAAGATGCTCTTAGAGCTTGTTCAAGAGATGAGAGTGGGAAGCCATATCCCATACAAGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001910:ENSGALT00000002951:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.145 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF139211=Myb_DNA-bind_6=PU(45.9=50.9)
A:
NA
C2:
PF139211=Myb_DNA-bind_6=PD(8.2=10.0),PF116263=Rap1_C=PU(23.5=48.0)
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:
GACGGCGCAGTTCAGAAGAG
R:
TGGGATATGGCTTCCCACTCT
Band lengths:
296-518
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]