GgaINT0039876 @ galGal3
Intron Retention
Gene
ENSGALG00000002090 | GPSM2
Description
NA
Coordinates
chr8:1335517-1336017:+
Coord C1 exon
chr8:1335517-1335679
Coord A exon
chr8:1335680-1335799
Coord C2 exon
chr8:1335800-1336017
Length
120 bp
Sequences
Splice sites
5' ss Seq
AATGTAATT
5' ss Score
1.5
3' ss Seq
TCCTTCTTCTTCCCTTATAGCCT
3' ss Score
10.8
Exon sequences
Seq C1 exon
AGAAACAGTCGAGAAACAGTGGCAGACGAAGGGTTCTTTGATCTGCTGAGCCGATTCCAGAGTAACAGGATGGATGATCAGAGATGCCACTTCCAGGAGAAGAACAGATTCTCAGCTGCTTCAGTAGCAACATCCTCTACTCCACCTAAAACAATACAAAAAT
Seq A exon
GTAATTTTAAAATTAAGATCTGTAGCTGACTTCAGTTCCCTTTCAAATGCTGTTTTAAAAATGTATTTGAATGGAGAGGAACTTCTATGCTTATTTGTTTTCCTTCTTCTTCCCTTATAG
Seq C2 exon
CCTTTTCTGCTTCCGTAGTCTCACCCCACACTGATGAATTTCTGGATTTACTTGCGAGCTCACAGAGCCGCCGCCTCGACGACCAACGTGCCAGCTTTAGCAATCTGCCTGGCCTTCGTCTTAACCACCGCACCAGTCCGTCTGTGCTGGGCCACTTAATGGCCAGTAACAACAGAGAGCTAGATGAGGACTTCTTTGATATATTAATAAAATGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002090:ENSGALT00000003258:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.364 A=NA C2=0.342
Domain overlap (PFAM):
C1:
PF0218812=GoLoco=WD(100=41.8)
A:
NA
C2:
PF0218812=GoLoco=WD(100=31.5),PF0218812=GoLoco=PU(47.8=15.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTGAGCCGATTCCAGAGTA
R:
GTGGTTAAGACGAAGGCCAGG
Band lengths:
248-368
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]