GgaINT0078880 @ galGal3
Intron Retention
Gene
ENSGALG00000009896 | TRERF1
Description
NA
Coordinates
chr3:24028990-24029923:-
Coord C1 exon
chr3:24029784-24029923
Coord A exon
chr3:24029094-24029783
Coord C2 exon
chr3:24028990-24029093
Length
690 bp
Sequences
Splice sites
5' ss Seq
GAGGTACAG
5' ss Score
6.62
3' ss Seq
TGTGGACTTGTTTCTGACAGTGG
3' ss Score
5.75
Exon sequences
Seq C1 exon
ACGAATTAATATTGGGTCCAGGTTCCAGGCCGATATTCCTGAGCTTCAGGACAAACTGCTGATGGAGAAAGATGTGCACAAGGCTACTCTGGTTTGGAAACCGTGGCCCGAACTGGAGAACAAAGTCTTCCAACAAAGAG
Seq A exon
GTACAGTGACTTGCTGGTTTAGAAGCTCATGCATCACCTTGTGCCTACTGAAGAAATTTCTGTTGATTTTTCATTTGTATACTGTACAAAACAGTCAAGAGAGCATTAATTACTGAGAGCACAGAGCAAGCGACCAGAACTACATATTACAGATTCAGAGTAACGTAGGCCTTTAAAGTGAAGTGCGGATGAAGTATTCTCTGGTAGCCACCAGGCAAAGGTCATTGCTGAGGTTTTTGGGCAATGAACTACTTGATAAGGGCAGAGATCACAGATGAGAGGTGGCTCCTGGGTTTGTCCTGTGACCATAACATAAAATTTGATTGTCTTAATGACCCCTTCTAGACCTGAGCAGAGTTTGCTCCTGCTTTTAGCGCAGTACTTTCCTCCAACGACAGGTTGGAGTCGTCTTGGTGCAGGAACATCACTGACTATATCTGCCTGTGCAAGCCACTGCTCACAGCCAGGCCTCTGCCTCTAGCTCTGTAATACCCCATCACAGCCCAGGGGTGCACTCTGCAAATCCAGGCATATCCTTTCCTCAGAGAGTGATAGTTGCTGGGGAAGGAGAATATGAAAGCTGCTGCCCTGAACTACGTTGTCTGTGAGTGACATTGCAGGATCCTTGTCTCAGGTTGTTTAAGTGACAGGTACTGTATTGACAATAACATGTGGACTTGTTTCTGACAG
Seq C2 exon
TGGAAGACCTCTTAAATATGAGCTGTTCCAGCGTGTTACCTGGTGGAGGAACTAACTCAGAATATGCTTTGCACTCTCTCTTTGAGGCAAAAGGAGATATTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009896:ENSGALT00000016090:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.104 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0144819=ELM2=PU(78.9=93.8)
A:
NA
C2:
PF0144819=ELM2=PD(19.3=31.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGAATTAATATTGGGTCCAGGTTCC
R:
ATCTCCTTTTGCCTCAAAGAGAG
Band lengths:
238-928
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]