GgaINT0124004 @ galGal3
Intron Retention
Gene
ENSGALG00000001797 | GPSM1
Description
NA
Coordinates
chr17:8612863-8614651:-
Coord C1 exon
chr17:8614492-8614651
Coord A exon
chr17:8613072-8614491
Coord C2 exon
chr17:8612863-8613071
Length
1420 bp
Sequences
Splice sites
5' ss Seq
TACGTAAGC
5' ss Score
5.9
3' ss Seq
GCTCCTCTCCCCCCTCCCAGCAC
3' ss Score
8.55
Exon sequences
Seq C1 exon
AAGATCAACCGGACCCCTTCGGATGAGGAATGCTTCTTTGACCTGCTGAGCAAGTTCCAGAGCAACCGGATGGACGATCAGCGCTGCCCGCTGGAGGAGTGCCCGTCGGAGGCTGCGGAGGCAGCAGCCACACCAGTCCCAGCCCTGGAAGAACGGATAC
Seq A exon
GTAAGCGTGGAGGTGTTGATAAGTCGCTGTGACTCCGGGTCGTGCTGCTCCCACGGCATGGCCGGCTGCGTGGTGCTGCTGTGCAATGGCCCGGGTGGGCTCTGGCAGGAGGGGAAGGTACTGCTGGGCGTTCTGTGTGACCACAGTGGAAAAACTTCTGGGTTTTGTCCAGTTGTTGGATGCTGCAGTGATAGGTGTTGCGTAAGGACAGAGAAGGCAGCAGGGCGGATGGATAAACAAGAGGAAGCTCCGGGTGTGCAGACAGCAAGCTTTGCTTGTGGGAAGAACAGGGATAAATGGAGGAAACCATCTGACAAATAGATGGGATGGGGAAGGCAGGCCAGGGCTGTGTCTGCGCTTCGGGTTTGCGTCTGTTTTGATGACAGCGTGTTGAGGTGCTCTGATTAAAGCAAACAGGAGCGAAGTGCTGGGGTGTGCAGGTCCTGCTGTGTGCTCCCAGGTGAGCCATTTCTTCTGGGCTAAAAATAAGGTGGAAATGAACATCGCTTTTTCAAGATGTGTTTCTGATGTAGAAATGCATTTGGCTGTAACAGCTGTGTGACTTAAGGGTGAGTTTGAGTATGGAGCTTTATTAAGAGCGTTCAAGTAGGCATGCTTTCTGTTCATCCATCACTTGGTCTCTGAGCTTTTTGGACGCGTTGTTTGAAGTTTCTTTGTCAGTGCTGCAGTTACTGTGCATTCCTACAACTCCAGGAGCTGGGGCTGTCAGAGCAGCAGTGTCAGGATCTTGGGGGACCCTCATGTGCTTTGTGCTCCCTGAGGCGATGCCCACCAGGCTGGATTTCTTACAGCTCCCCTTGCTTGTCCCCATCCCAAGTGCAGTGCTTGTTGTGTGAATGTTTTGCTGCCCAGCAGCTGCTAGGAGCCAGGAGGCCCCATGCATTGCGTGCTGCCCTGGCTGGGGCATTGCTGGGATGGGTGGCTTAGTCAGGCCTTGGCTTTGCACATTACATGCCTGCAATTATACCCAGCCCTTGGCACCATGTGCAGTGTCCAGTAAGGAACCACAGCAGTGCACAGGAACTGTACACTCACCTGCAACTGCTGCTGCCTGCACCAGGGTGGAAACCAAGGCAGCAGCAGCATCCTGCCAAGGTCTCTGCCTTACCCTACATACTAGGCAATGCAGCAGAGGCACTAGAGAAGGGTGTGAGTGGTTGCATGCTTGGGTCTCTGCTTTGGTGGTAGGTTTTTGCTTGCTTGCGTTGTTGGCACTGGGATTGTTCCTGCTTATTGCACAGGGTGGAAGGGAATGGTGCTGGTCACAGAAGCTGGGGTCCTACCCAGCTCAGCCCTGGGAGGCTTCTCAAACAGGGGCTTAAGTCTGTTGGTGAGAACTTGAGAAGACTCTGTGGTGAGCAGAGATGTGACCCTGGTGTGCTCCTCTCCCCCCTCCCAG
Seq C2 exon
CACACTCCTCCCTGATGGCATCCCCACAGACGGAGGAGTTCTTCGATCTCATCGCCAGCTCGCAGAGCAGACGGCTGGATGACCAGCGTGCCAATGTGGGCAACCTGCCAGGCCTGCGGATAACACACAACAACCTGGGGCACCTGTGCATGGAGGGGGACGCCCAGGAGCCTGGGGATGAGTTCTTCAACATGCTGATGAAGTGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001797:ENSGALT00000002770:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.574 A=NA C2=0.500
Domain overlap (PFAM):
C1:
PF0218812=GoLoco=WD(100=42.6)
A:
NA
C2:
PF0218812=GoLoco=WD(100=32.9),PF0218812=GoLoco=PU(68.8=15.7)
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:
AAGATCAACCGGACCCCTTCG
R:
TGAAGAACTCATCCCCAGGCT
Band lengths:
349-1769
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]