GgaINT0035813 @ galGal4
Intron Retention
Gene
ENSGALG00000004424 | SEC16B
Description
protein transport protein Sec16B [Source:RefSeq peptide;Acc:NP_001026440]
Coordinates
chr8:6599726-6600367:+
Coord C1 exon
chr8:6599726-6599877
Coord A exon
chr8:6599878-6600305
Coord C2 exon
chr8:6600306-6600367
Length
428 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
AATTTGCTCTTGATTTTCAGGTA
3' ss Score
9.27
Exon sequences
Seq C1 exon
GAGGGCCCTTGGAGTCAGCTGTGATGGCACCCCACAAGTTCCTGCAGCCACATGTGCCCGTCTGCTTGGGAGCTGGAGGGCAACTGGTGCTGGTGTGTCCCCACCGTCCCACTGAGGGGCAGCTCCCCCTGGTTGAGCTGCACAGCCTGGAG
Seq A exon
GTAAGCCCTGATTCCCCAGACAGCCTGTGGTTCCCTCCCTTGAGCTGCCCCTTCCACCCCAATGGGGTCAAACACCATTCCTTGCCTCAGCGGACCCCTCAGCCACCTTTCTGTCCCCGCTGCCATCTTGCCTCCAGCCCTCATGGCCTCTCAGGCCTCATTCTGTCAGCCATATCCATTCCCTGAGTCCACCACACCTCCCTTCCTTGCCTTGCAGATGCCATCTCAACAGCCTGGTCCTTAGCACTGGATTGGATTCTATGTGATGGTTTAGGGTCTGTACTGTGGGGGTTACTTTATGATGGCATGGAGATTTTGTTCACCAACACAGTTAAACCCTTGGTCAAGGCACTAAACATTCATCTAGTCAATGAGGGTGCTAGCCTCGTTTCTGGAGTTCAGCTGCTGAATTTGCTCTTGATTTTCAG
Seq C2 exon
GTAATCCTTCAAGGCACAACAGATCAGGAGGAGCTTCAGGCCTTCCCAGGGCCTCTGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004424:ENSGALT00000007046:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.059 A=NA C2=0.238
Domain overlap (PFAM):
C1:
PF129322=Sec16=PU(33.3=66.7)
A:
NA
C2:
PF129322=Sec16=FE(19.6=100)
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:
GCCCTTGGAGTCAGCTGTGAT
R:
CCTGGGAAGGCCTGAAGCTC
Band lengths:
198-626
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]