GgaINT0035822 @ galGal4
Intron Retention
Gene
ENSGALG00000004424 | SEC16B
Description
protein transport protein Sec16B [Source:RefSeq peptide;Acc:NP_001026440]
Coordinates
chr8:6604601-6606325:+
Coord C1 exon
chr8:6604601-6604741
Coord A exon
chr8:6604742-6606211
Coord C2 exon
chr8:6606212-6606325
Length
1470 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CCCGTGTCCCTGCACCACAGCTG
3' ss Score
7.73
Exon sequences
Seq C1 exon
GTGTACAAGCTCCTCTATGCCTCCCGCCTGGCTGACCATGGGCTGCCAGCCCAAGCCCTGCTCTACTGTGAGCAGATTGCTACCGTGCTCCTCCAGCAGGACCCAACCAGCCACCCTGTCCTGGCCCAGCAGCTGACCAAG
Seq A exon
GTGAGTCTTGTGCCTTTGTCATGTGGATCTTGCATGGGGATGTTGCTGGGGGCCTGCTGGCTCGGGGATTTCACATGGGTGCCTATGCTCATCGACATGTTTTATGCCAGATAGGGTAGGAGCTGTTTGCAGACAAAGGACTTCGGGGTTTGGATGTCCCCAAGTCACCTCCCCCAGGTGCTCATTGTCCCCACACTTGGGCATCCAAGCATCCCATGTCCCACAGGCTGCACACCTCCCACCATGACAACACCTTGGCGTGGGCAGCCGGATGCTGCTGTGCTGCAGGAGCTGCCCCCAGCCCCAAAACTTGGTGCTGCACACCGCAGCCCCCCTGCTGCATCACAGAAACCTATTTACTGCCTAACAGCCTCTCAGATCTGCAGTTCTGCTGGGGATAATGCTCCTCCTGGGAGAAAACACTTTCATCTGAAAAACCAGTGCATTCATACACACTCTTGTCTTTGATGTTTTAGACTGTGTTACAAATTATGATACACATTAGTGTTTGATTAAGACTTCCCCTCTTTTGAAGCCGGGGACGGTATACAACCAGGTGCTGGTTCATTAATATTGGATCAAAGTGCACATTAGCTTTTGGATTAAACATTCCCCCCGTTTAGGAGTAATCATGCTTATAATTTCCTCTTTCCTGCTATTGATTTGGGATGAGTGCAGGCTTGCACAAAGCTGGGACACACAGGGGTCCGGCTGTGCTGGGTGGCTCTGGCCAGTCCCTGTCCCCAGCATGTGTCTCATCTGGCTGTCACCAATGAATCACAGCATTGTTTGAGCTGAAAGGGTCCCTTAAAGGCCATCTGGTCCAACCCCCTGCACTGAGCAGGGACATCCACAGCTCCATCAGGTGCTCAGAGCCCCATCCAGCCTGACCTTGGCTGTCTGCAGGGATGGGGCACCACCATCTCTTTGGGCAACCCATGCCAATGCCCCACCAGGATGTGGGCGCAGACCCTTCTCATGTTGGAGAAGCAAAACGTGCAGCAGTACTGCAGTGAGGGACATGGGGGAGACAGCGGAGCGTGGAAAAAATACAGAGCACAACATGACAGCAGGATGCTGTTGGTGGGGGGGGGGGGGAGAGGGGAAAAAAAAGAAGGTGATGTTATCATGTTATTCTGGGCTGTGAGAGCACGAATGGCATGTGTGAGACAAGGAGGTGATAATCCCCCATGCTTGAGGGTCTCAGCTGGGGCCCTGTGCCCTGTTTCGGATGCGCAGCACAGGGATAGTGCCAGATTGGTGCAGAAGAGGAGAGCTCAGTGATAAGAGGTGAAAGGAAAAATGACCTCAGGGTTGTTTTCTGCAAGCAAGATAAGGCGGAGAGGAAAAGGGTGCAGGGGGTTGTGATACAGGTCTGCCAGTGTGTGGGGAAGCTGGTTTTAGGGAGCAAGGATCGAGAGGCTTAATTTGCAGTGAGGTCAGGAACAGCCCCGTGTCCCTGCACCACAG
Seq C2 exon
CTGGCCGAGCGACTGAAGCTCTGTGACCCACTGCTGCTGGAGATGCCTGAGCAGGACCCGGTGCTGGAGCCCCAGTGGCTGCTGCAGCTCCGCACCTACTGCCAGCGCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004424:ENSGALT00000007046:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF129312=Sec16_C=FE(19.2=100)
A:
NA
C2:
PF129312=Sec16_C=PD(3.3=21.1)
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:
ACAAGCTCCTCTATGCCTCCC
R:
CAGCGCTGGCAGTAGGTG
Band lengths:
247-1717
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]