GgaINT0035807 @ galGal4
Intron Retention
Gene
ENSGALG00000004424 | SEC16B
Description
protein transport protein Sec16B [Source:RefSeq peptide;Acc:NP_001026440]
Coordinates
chr8:6597575-6598339:+
Coord C1 exon
chr8:6597575-6597734
Coord A exon
chr8:6597735-6598092
Coord C2 exon
chr8:6598093-6598339
Length
358 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
ATGGGTCTTGTTGCCTGCAGGCC
3' ss Score
9.11
Exon sequences
Seq C1 exon
TTTTTTTCCCTTTTTTTTTGAGCTCAGAGGTTCATGTGCTCTATCTCAGGTGGGAGAGCCTTGGCTGGTCCCTGGGCTGGGCTGGGAGCTGCTGCCCTTTGTCCCCTGCGGTGGCAGTGGACTTTGGCAGTGGCGCCGGGGAGCGGAAGTGGGGCAGCAG
Seq A exon
GTGTGTGTGTGGCTGGTGGGGGGTGGTGGGGACCCCCGTCCTACGTGGGATCCAGGGGACCTGCGCCAGGGTGGGAGGACTTGCTGGGTCCAGCTGGGCCCAGAATGACCCCCAGATGCATTAAATTCTGAGTGCGAGGGGGCGATGTGTGGTTTGGTGATGGCTCCTTGCATCCTGGTGTTTTAGGAAAGCTTCAGGTGGAACCAAAAGGGAAAATACATGTTTTACCCCTGCTTCTGCTGTAGGCGTTTTGGGAAGAAAGGACGGCAGTGGGGTCGGGAGGTGGGTGGAAGGTTTACAGAGGTTTTGGGGTGGGTGGAGAGCTGAAACCTGCAGGGATGGGTCTTGTTGCCTGCAG
Seq C2 exon
GCCATTGGAGCCGTTGGATCTGCTGCATGGAGCCCTGGGACCCACCACAGCTGCCCCCAGTGCGGCACAGCCATGCTGCTGGCAGTGGGCGGGCAGAAGGCCGCCATGGGACCCCACCGCCCTGGAGGCCCATCATCTCTGGCCCCCTGCCTCGTCCTGGCTCCTGGGACCCTGGCAGGGACCTGCACTGGCCAGCGTCCCAGGCTGAGAGCTATGAGAGCGGCCATGCCTTCCGGGCCTACTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004424:ENSGALT00000007046:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.590
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
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCAGAGGTTCATGTGCTCT
R:
TCATAGCTCTCAGCCTGGGAC
Band lengths:
356-714
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]