GgaINT0035812 @ galGal4
Intron Retention
Gene
ENSGALG00000004424 | SEC16B
Description
protein transport protein Sec16B [Source:RefSeq peptide;Acc:NP_001026440]
Coordinates
chr8:6599385-6599877:+
Coord C1 exon
chr8:6599385-6599514
Coord A exon
chr8:6599515-6599725
Coord C2 exon
chr8:6599726-6599877
Length
211 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CTGTTTGTCTTCTGCTTTAGGAG
3' ss Score
11.16
Exon sequences
Seq C1 exon
CCCAGCCTACTCCAGCAGTACCGTGAGTCAGGACTCAGCTCCAGTGGCTATGAGCTCAGCCAATACATCCGCGATGGAGCCGAACCCAACGACACTGCTTTTTTGGGGGGCTGGAGCCCGGTGCAAGGAG
Seq A exon
GTGAGGGCAGCTGGGGGTCTTGGTGAAGCTCTGGCAAGGGGGGAGCAAGTAAATAAATAGCAGATCTCCTAGCAACAACTGTCTCATAACTTGAACCTTGGCTGGAGGAGGTCCAGCAAAGGGTGAGCGTGGCCTGTGGAGTGTCTGTATGGTTTGGTGGATTTGCCATGGTGGATGCAAGGAGCTGCCACCTGTTTGTCTTCTGCTTTAG
Seq C2 exon
GAGGGCCCTTGGAGTCAGCTGTGATGGCACCCCACAAGTTCCTGCAGCCACATGTGCCCGTCTGCTTGGGAGCTGGAGGGCAACTGGTGCTGGTGTGTCCCCACCGTCCCACTGAGGGGCAGCTCCCCCTGGTTGAGCTGCACAGCCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004424:ENSGALT00000007046:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.455 A=NA C2=0.059
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF129322=Sec16=PU(33.3=66.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTACTCCAGCAGTACCGTGA
R:
CTGTGCAGCTCAACCAGGG
Band lengths:
270-481
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]