GgaINT0078876 @ galGal3
Intron Retention
Gene
ENSGALG00000009896 | TRERF1
Description
NA
Coordinates
chr3:24036559-24037895:-
Coord C1 exon
chr3:24037739-24037895
Coord A exon
chr3:24036808-24037738
Coord C2 exon
chr3:24036559-24036807
Length
931 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCA
5' ss Score
6.37
3' ss Seq
GCCTTTAATTGTCTGTACAGGAT
3' ss Score
8.7
Exon sequences
Seq C1 exon
CAATAGTGGCCCAAACAGAGAAACACTTCCTGAGAGAGCTGACGGGAAGAACAAGCTAACGTGTTCAGTATGCTTGAAGGAATTTAAGAGTTTGCCTGCTCTGAATGGTCACATGAGGTCTCATGGAGGAGTGAGAACATCTCCTAACTTCAAACAG
Seq A exon
GTAGCAGTTTATTTTACCTCGGTATTTGATTCTCTTCTCTCCATGTTGATGTTTGCTTGCTTTGCCACGCTTTGCTTTGCTATCATACCTGTTCTCCTCTGCACTGTTTTATGTCACACCCCGTTTATGTAGAAGCACACATAATTCTGATGATTTACAGTCTCACCTAAAAGTGAGAGATGGTGGAGGACAGAACAACATTTGTGCCTCTTTATGTCTCTGCACATTACAAAAACACTCTACAAAATCATGGCACAAGCTTCTGAATTTTTTCCCCTCATGTTTGTTTATTATATCAGAAATATCAGGAACATCAAGTCTTCCTTATTTTCGTTTGGACTACTTAGATGACTAAGGAATGTTTATTGGAAGCATTCCCAGGCTTTAACTGAAGGAGCAGGATTGTTGAATCTTTGACAGCTTCCTTCTCCTTCCAAAGTGTTGTAGTTCTGTAGGTATCAACAAATACCAAATGCAAACTGTGGGTTTGAATTGTTCTGAATAAAGACAACTTGCCCCATCAATCAGTTTTTCAGTGTCCTGATATTTGAAAAATTCTCTCTTGATGGGGGAGTACTACAGAAAGCCAAAGAGCTACCAGGGTTGCACCATGTCTTTTTTGTTCTACGTGAGCGATGGGGAATTCTGCCTTTATAGTGTTAAAAGAAGGGCATGTGTTTATTGCCCCTTCTGCAAGTGATCCTGTAAAGATGCTTAATGTGATTATTTGTCACTGAGGCTAAATCCTATATAGGAGTCAAGTAATCTGTCAACTTCCTTCAAGGCAAATACAGAGTCCAAGAAGCAAGGCTATTGTGTGTATTGTAACCCTGGCCTCTTCTTCTCAGCCACAGTGCATACACTGTATAGTGTATCAATCCAGAAGCGGCCCTCCCTCACTTGGGCTGAAAGCCTTTAATTGTCTGTACAG
Seq C2 exon
GATGAAGGAGAGAAACCACCACAGCAGCCGCTGCCTAAAGAGGTGGATAGCCTCGCGCCCATCGTCATGCCAGTGTCTGTCCCTGTAAAGCTTCTGTCACCCGAACCCAGCACGCAGCCCTCTGCCAGCACTACCACAGTCAAAGACAAGCCTGCCAACTCTATGTCAGATGATGAGATGCCCGTTCTCGTGAAGATGACTTTCTCTCCACCGTGCAGTCCAAAAGTGGCCAACCCCTGCTCATCCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009896:ENSGALT00000016090:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.755 A=NA C2=0.892
Domain overlap (PFAM):
C1:
PF139121=zf-C2H2_6=WD(100=45.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGAGAGAGCTGACGGGAAGA
R:
CTGCACGGTGGAGAGAAAGTC
Band lengths:
346-1277
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]