GgaINT0127842 @ galGal3
Intron Retention
Gene
ENSGALG00000004333 | E1BY40_CHICK
Description
NA
Coordinates
chr18:7981102-7981635:-
Coord C1 exon
chr18:7981460-7981635
Coord A exon
chr18:7981222-7981459
Coord C2 exon
chr18:7981102-7981221
Length
238 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
TCTGCTTCCTGTGTGCAAAGGTG
3' ss Score
7.46
Exon sequences
Seq C1 exon
GGTTTGTCTCTGTCTATGGGCACAGAGTCTCCGAAATCGACGAGATGCTCGAAGTGCGGCGCATCGCAGGCGTGTGCCCACAGTCCGACATCCACTTCGATATATTGACGGTGGAGGAGAACCTCTCCCTCTTCGCTGCCATTAAAGGAATACCTCAGAATGACTTGATACAGGAG
Seq A exon
GTAGGTGGCTTGTACCCCAGTATTATGTTATATCACAGAACTGAAGAATCTTGAGGTTGGATGAGAGAGCTTGGGACCATCCAGTCCAATGATGACCCATTCGTTTTTTCCTAGCAACCTAAAGCACACACAAAACATTTAAATCCTAGCATTAATTTGAGTGCTAAACATTGTAAACTAGTTTTAAAAAGCCCGTTTCTTGTTTTTTAATCAATAAATCTGCTTCCTGTGTGCAAAG
Seq C2 exon
GTGCAGAAGGTGTTGCTGGATTTGGATATGCAGCCCATCCGAGATAACCAAGCCAAGAAGCTCAGCGGGGGACAGAAGCGACGGCTGTCAGTTGGCATTGCTGTTCTTGGGAACCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004333:ENSGALT00000006907:12
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:
PF0000522=ABC_tran=FE(39.5=100)
A:
NA
C2:
PF0000522=ABC_tran=FE(26.5=100)
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:
TGTCTCTGTCTATGGGCACAGA
R:
TCCCAAGAACAGCAATGCCAA
Band lengths:
284-522
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]