GgaINT0125640 @ galGal3
Intron Retention
Gene
ENSGALG00000004622 | C9orf114
Description
NA
Coordinates
chr17:5910242-5910657:-
Coord C1 exon
chr17:5910608-5910657
Coord A exon
chr17:5910373-5910607
Coord C2 exon
chr17:5910242-5910372
Length
235 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
TTTCCTGTGCACTGTTCCAGGGC
3' ss Score
9.22
Exon sequences
Seq C1 exon
GTACTTGAGGAAATCATTTTTTCCAAAACATGGGGATCTGCAGTTTGCAG
Seq A exon
GTAATGATTCAGTTCTCCTTGTCCCAAGCTGTTGACTCCCCTTCCACAAGCTCTGGCTCTCATTTTGCACAGAATACATACAACTTAAAGTCTTTTCCCTGCCATGTAGCACAGGTGAGATACTGTGCTCCACTGGAGAAGAGAGGGAGGAAGAAGCAGAGCAGCTGTACTTACACCTGTGTTCCCATAGTCCGTATTCTGTCCTTAGCTGTTGCTTTCCTGTGCACTGTTCCAG
Seq C2 exon
GGCTCCTCAACCCACTGGACAGCCCCCACCACATGCGGGTGGATGAGGATTCTGAGTACCGAGAAGGTGTGGTGTTAGATCGGCCAAGCAAGCCAGGCAGAGGCTCATTTGTCAACTGTGGGATGAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004622:ENSGALT00000007359:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.205
Domain overlap (PFAM):
C1:
PF0259812=Methyltrn_RNA_3=FE(5.8=100)
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=FE(14.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAAAACATGGGGATCTGCAGT
R:
CTTCTTCATCCCACAGTTGACA
Band lengths:
159-394
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]