GgaINT0020566 @ galGal3
Intron Retention
Gene
ENSGALG00000001535 | STAB1
Description
NA
Coordinates
chr12:592864-594989:+
Coord C1 exon
chr12:592864-593000
Coord A exon
chr12:593001-594873
Coord C2 exon
chr12:594874-594989
Length
1873 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CTTGGATTGTTCTTTTTAAGGTA
3' ss Score
8.78
Exon sequences
Seq C1 exon
TTAAAATCAATGAAATGCAACGTCAAGATGACATATACCTCAAGCACAGCATGTACATCTTGTGCTGCGGTGCCTAGGATGTCCTGTCCCAAAGGCTGGATGAGGGCCACCCAAGGACGTGGAGTGAGGGGCTGCAG
Seq A exon
GTAAGACGCTCCCTAAGCAGTCATGGTTTTGGTTTAGCCCTGCTGTGCAAGGGGTAATAGTAATGTGTATGGTTTTTGAGCTCTAACGATCCAAGCAGTTTTGATTTCAGATGCACAAAATGGATTTATGGTCCCTATAAATGGCCCCTATAATATTTATGGCTTTAGTCTCCTTGCAAATCCCAGGGAGTTTTTCATGGTCTAAGGCTCTATACACCCGAAATAAGTTGTACGATGACTACCTCTGCCTTGCCCTGAACAACCTGGGTTTTCTAATCCTGATTTAGTAACTAAACAGAGTTCTGTCTACTCTCTAGAAACCCATTTCAGGCTGTTGTGGTTTAATCTGGCAGCAGCCCAGCACTGCAAATCCCCATCCCAGTGGGATGGAGGAGAGAGTCAGAAAAGAAACAAAGTAGGACTCACTGAATGAGATAAATACTCAATGCCCTTCCAGTATTTGAAGGGAGTATATAAGCAGGAGGGGATATGACTACGAGGGTGGATAGTATATAAGCAGGAGGGGATATGTTTACGAGGGTGGATAGTGATAAGACAAGGAGGAATGGTTTTCAACTGAGACAGGGGAGGTTTAGGTTGGATATTAGGAGGAAGTTTTTCACCCAGAGGGTGGTGACGCAGTAGAACAGGTTGCCCAAGGAGGCTGTGGATGCCCCATCCCTGGAGGCATTCAAGGCCAGGCTGGATGTGGCTCTGGGCAGCCTGGTCTGCTGGTTGGTGACCCTACACATAGCAGGGGGTTGGAACTTGATGATCATTGTGGTCATTTTCAACCCAGGCCATTCTGTGATTCTATGATAGAATTTCTTTACTAAGTAAGAAAGGGAAGAGGGGAAAAAGGGGGGAAAAAATGTCTCGTTCTTGTCTTCCTTGCTCTTATTCTGTTGAATGTTTCTATAGCTTGACTCTAGTAGGAAAAGGGTGAAGGAAAACTTAATTTATCCGTAAGTTTTTAGACAATGAAACACTATAAATTATTGTTTGCTCATCTATTCAGTAGTGAATGTTATGCAGTATATAGTTCCATTGTCTACTGTTTTCTGTGACTCGCTATTTTGTAGAAACACTTTAAAAATAACTGTAGCACTTGTGCAGTAACTACAGGAGTCAGGAGTCAGACAGAATCCAAAGCCAATTTCCAAGTTCCTTTTGGGGAAGGATGTTGTGCCAACAATAAAACAAAGTGTGAGAATAACCCAAGTGCAGACAGTTTTTCTGAGTGTTTGGGTGGTGGTGGGGTTGTTGGATAGACCCAAGTGTAGTTCTGTCCAGCACACATGCAGAGCAAAAGACAATTTGCCACCAAGGGCTTACCCTCTGTGTGAAGATAATGCATGAAGGGGAAAATGCTCCTTCCTGGGGACCCAGGGAGTATGTCCTTGATGGCATAGAGAACCCAACTAAAGAACACAGTTATTAAATCCAAATTTACAGCATACCAACGAGGAGTCATTACTGAAAGATAAAAGGAAACAAGTTTTGCAAGGAGATTTTATTCTTTCAAGTTCATTTTATCTGTAGAGTCTGAAGTCACCCTGGAGAGCATTACTCTGTCTCTATGCCATCTAACCATTCAGCATCTGCAGTTTCTGTCTGGATACCCTCAGACTTGCCCAGATCCTGTCTCACATTCGGTCCCTGGCAGAATTCTTACAGCCAGTCTTTGGAGCACAACAGGCATCCCTAGGGAAGATGTAACCAGAGGGGAAATTCCGTGTGCGTGTACTGGGGCTGGGAAGAGTTCTCTTCCGTTCAGAGTTCAGCGCACAGCAGTGTGCTTGCTTAGAAACCCTGCAATGAGTGTGTGGTGTGTTTGTGTGGTAATCACGAACCTTGGATTGTTCTTTTTAAG
Seq C2 exon
GTACACCGTCAAATTAGGAGAAAATACCCTCTCCCAGCCAGGGTGCTATCAAATATGTAAGAAGGAAATTGAGGAGAAAAAGTGTTGCCCAGGATTTTGGGGTACAGAGTGTTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001535:ENSGALT00000002333:3
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAATCAATGAAATGCAACGTCAAGA
R:
CACTCTGTACCCCAAAATCCTGG
Band lengths:
246-2119
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]