GgaINT0035808 @ galGal4
Intron Retention
Gene
ENSGALG00000004424 | SEC16B
Description
protein transport protein Sec16B [Source:RefSeq peptide;Acc:NP_001026440]
Coordinates
chr8:6598093-6598625:+
Coord C1 exon
chr8:6598093-6598339
Coord A exon
chr8:6598340-6598518
Coord C2 exon
chr8:6598519-6598625
Length
179 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
CATGTGTTACGCTGTTTCAGGCA
3' ss Score
8.62
Exon sequences
Seq C1 exon
GCCATTGGAGCCGTTGGATCTGCTGCATGGAGCCCTGGGACCCACCACAGCTGCCCCCAGTGCGGCACAGCCATGCTGCTGGCAGTGGGCGGGCAGAAGGCCGCCATGGGACCCCACCGCCCTGGAGGCCCATCATCTCTGGCCCCCTGCCTCGTCCTGGCTCCTGGGACCCTGGCAGGGACCTGCACTGGCCAGCGTCCCAGGCTGAGAGCTATGAGAGCGGCCATGCCTTCCGGGCCTACTCCAG
Seq A exon
GTGGGAGCCGAGGGGCTGCTAGCACCGAGCCCCCTGCCTCATGGATGAATGTGAGCTCCAGAGCTCAGTGTGGAGGATGCTTTGGTCTCCTGCCCCGGAGATCCCATCTGTGGGTCTGTGCCTGGTGTAGTCCAGGCTCTGGTGGGAGGTTCTCAGCTCCATGTGTTACGCTGTTTCAG
Seq C2 exon
GCAAGGATATGAAGACCCCCACTGGCAATACCCAGGAGCTGCCTACAGGGACAACCATGCTTACCAAAGCCACCAGTGGCAGCCCACGGCCTGGCAGGGCAACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004424:ENSGALT00000007046:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.590 A=NA C2=0.595
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
CGTTGGATCTGCTGCATGGAG
R:
GTGGGGGTCTTCATATCCTTGC
Band lengths:
258-437
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]