GgaINT0123999 @ galGal3
Intron Retention
Gene
ENSGALG00000001797 | GPSM1
Description
NA
Coordinates
chr17:8642471-8643862:-
Coord C1 exon
chr17:8643707-8643862
Coord A exon
chr17:8642580-8643706
Coord C2 exon
chr17:8642471-8642579
Length
1127 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
AGCAGCTTCCTGTCTTGCAGGGT
3' ss Score
7.68
Exon sequences
Seq C1 exon
GAAGACACTCCAGCTCTCCAGACAACTCAAAGACCAAGCAGTAGAAGCCCAGGCTTGCTACAGTCTTGGAAACACGTACACACTGCTTCAAGACTATGAGAAAGCAATTGAATACCATCTAAAACACCTGGTGATAGCACAGGAGCTGGGAGACAG
Seq A exon
GTAAGGGAATGCCTCCAGGGGTGGTTTCTCTGTTCTTGGGCTGTTCTCTGAGTGCTGTGCTGTCTCTGTTATCTATCACTGTGTGCTGCTGGAGATGAGGAATAGCAATGTGTGATACTGAGGGTCTTCAGCAGTCTCTCAGGAAGTGGTCTTTGGTCCTATCATTGGTCAGGGGAGTAAAAGTGATGTGAATGAGACCTTTATCATCCCACTGAAACCCAGAGGTCGTGTCCTTATGCCTGCGCCTTCTTGTTCGGCATCACTTCCAGCAGCCCTGGGAAGCTGGGCGTCCTCCACTAGATGGAGCAGGGAGACACAGATAGGAGCACCTTGGCGCTGTCAGGGCAATATCTGCACGGGGAAGATCTAATCCCACCCAAGGGTGAATCATGCTGTGGGGGTGCAGCCTTGTGGGCTCCCGCATTTCTGGGAACACGCCCCGTGAGCAGAAGGCATTGAACTGGGTGACAAGAAAAACGTTTAAATGCTGATCAACCCGCCCCAACCCCTGAGGAGGGAGTTGCAGTCACGCTGAACCTCCCCCCGCGCCCCCATGTGCTTTTTTTATCCCTTCACCCCCCACATCTGCACGTTGGCAGAGCTGAGCAGGCTGTGCTGAGCAGCCGGGCTGTGTGTGCTGGTGCAAGCAGGTGCTGGAAACACACCTGTGTGCTGGGTCAGGGCTGCCCAGTGACATGCTGGTATCCAGCAGGGGGACGTTGCATCCCTGTGGTGTGGGAAAACCACTTGCTGGATGACAGCCGTCCTCTTGATGCCTTTTGTGCCCCTAGAGAGGAATCCATGCAGCGCAGAGCAGATGGGAGCTCTCACTTCTGCTCTGATGGATGCTCGTGTGTGACGTCAAACTGTTCTGGGTCCTTGCTACACCACCTAGCTTTTGGCTGCTATGGGTACAGCCCCATTTCTGAAACTATTGCTTGTCCCCTCACCTCACTGCCTTTAGTGTAAGGGATTAAGCTGCACAGTGTGCATTTTTTTTTAGGAGGATACTCTGAGGGTGAAAGCAGAGCTGGCTCAAGGTGCTGCTGAGGAGGCTGTGAAAGGGCTGCTGTGCTGGGTTGGGCTCTGCCCAGGATTTCTGTGGTCAGCAGCTTCCTGTCTTGCAG
Seq C2 exon
GGTGGGAGAGGGAAGGGCCTGCTGGAGTCTCGGAAATGCCTACGTCTCCCTGGGGAGCCATGAACAAGCTTTGCACTTTGCAAGGAAGCATCTCGAAATCTCCCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001797:ENSGALT00000002770:7
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:
PF134241=TPR_12=PD(61.5=90.6)
A:
NA
C2:
PF134241=TPR_12=PU(56.9=89.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGACACTCCAGCTCTCCAGAC
R:
TCTTGGGAGATTTCGAGATGCT
Band lengths:
262-1389
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]