GgaINT0123997 @ galGal3
Intron Retention
Gene
ENSGALG00000001797 | GPSM1
Description
NA
Coordinates
chr17:8644101-8645170:-
Coord C1 exon
chr17:8645047-8645170
Coord A exon
chr17:8644217-8645046
Coord C2 exon
chr17:8644101-8644216
Length
830 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGA
5' ss Score
4.3
3' ss Seq
TTAATCTGTGTCTGCTGCAGCGC
3' ss Score
10.29
Exon sequences
Seq C1 exon
GAGGAACCTGTCCCTGGTGAAGGAGCTGGGGGACAGAGCTGCACAGGGCCGTGCTTATGGCAACCTTGGCAACACGCAGTACCTGCTTGGCAACTTCAGCGAGGCCATCGCCTTCCACAAGGAG
Seq A exon
GTGGGAAAGCACGTGGGGATCTTCCTGGGGGCTGCAATGGCCAATAGGGAGCAGACCTTTTGCTCAGCTCTGGAGGGGCACAGACCCCCATGTGTGTGTCAGTCCCTGCCCTGATGTGCTGTGCTGCCTTCCTGCTTTCCTCATCAGCACCTGACGAGCAGTGCGAGGGAAGGGTGCTGTTGGCTTGGAAACCAAAGGAGATTTCTAAGGGCAATTTGCAGCTGGGCCTGGGAAGGGCTTTTCTGTGCTTAACTTGTGCCAGTCTAAATTTTAATAAATGCGAGCTGTGAATTTAATTAAGCTGCTGAAAGAGCTGCTGATCAGGAATAACTGTTGTTTGTAGAGCACAGCTACTTTCTGTAAAGCTTTTCGGAGGGGTGAGACCAAACAGTCCCTGCCCCAATTCAAATGCAATTCAGTTTCTTGTTGAGAGCTGACGCTGTTTCTTTCAAAGCAGAGGGTGCAGAGCATATCATGCAGTCAGACCCTGCCATGGCTGCTCTGGTTTTGTTTGAGGAGGTGCTGGGGGCGGCAGTGCTGCGAGAGAAGGTGTTTGAAAGGGACAGGACAACTGTGCAGCCCCTTCTGAAGCCAAACGGGGCAGGCTGGGGGGGGTTTGCAGGAGGATGTGTCTCTGCTCCATGTCCCTCCTGATGCTGAGCTGCAAAAGACGAAGAGTTCCTGCTGCATCCAGCCCTGACGTGTAAATGCACGCTGCATTTCTGGATGTGAACCCTTGCAAAACAGGAAGCTCATCTCCCAGCAAAGTTGCTGTGTAACAGAAGCCTGGCAGTGCCTGCCTGTACTCCATTAATCTGTGTCTGCTGCAG
Seq C2 exon
CGCCTGGCTATCGCCAAGGAGTTTGGGGACAAAGCAGCCGAGAGGAGAGCATACAGCAACCTGGGCAATGCACACATCTTCCTTGGGAGATTTGACATCTCTGCTGAATACTACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001797:ENSGALT00000002770:5
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=FE(66.1=100)
A:
NA
C2:
PF134241=TPR_12=PD(9.7=15.4),PF134241=TPR_12=PU(37.2=74.4)
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:
GGAACCTGTCCCTGGTGAAGG
R:
TTGTAGTATTCAGCAGAGATGTCA
Band lengths:
238-1068
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]