GgaINT0125638 @ galGal3
Intron Retention
Gene
ENSGALG00000004622 | C9orf114
Description
NA
Coordinates
chr17:5910955-5911764:-
Coord C1 exon
chr17:5911605-5911764
Coord A exon
chr17:5911045-5911604
Coord C2 exon
chr17:5910955-5911044
Length
560 bp
Sequences
Splice sites
5' ss Seq
AAAGTAGGG
5' ss Score
2.67
3' ss Seq
CAGACTGTTCTCTCTTTCAGGAG
3' ss Score
10.94
Exon sequences
Seq C1 exon
GGCGGCACTACACGCTGAGCGTGGCCCTGCCGGGCTCCATCCTGAACAACGCGCAGTCGCTGGAGCTGCGGACGTACCTGGCCGGGCAGATCGCTCGAGCGTGTGCCATCTTCTGCGTGGATGAGATCGTGGTGTTCGACGAGCATGGAGAAGATGCAAA
Seq A exon
GTAGGGATGAGCTGTTTTGGTCTGCAGAAAGCTTCTCCTCTGCGCTCCTTCGGTCTTTTTTTTAGCTGAGATCGGGAAAGAAATGTCTGTACCCCGAGGAAGTGCTCCTACCACCACCATCACAGGGCCCTCTGGGGGCAGAGATGGTCACTTACCTGTGCTGGAGGCTGGGATACAGGGAAGATGGGGATGCTCTGAAGGGATGACACCTGTTCCTTTGACTTCTCATCTGGGCCTGTGCCTGCCTTCGCTGGCCAAGCACTGCAGTGCTGTAGAATCCAACTGTCAGGTTGTATCTAAAAACAGATACATAAAGATTAAAAATGACAACAACAAAAAAAACCCGAGTAAGATCTTTGACTTGGGGAGTTCCAAGTAGAACTTGTTAATAATCCGTACCTCTGGAGCAGCCCTTTTCTAAGGTAGCCCATTTATTTCTGTAGAGGTTGAGGGTGGAGGGAGCTGCCAGTCTTAGATTAAGAGAAGGGCTTGGTCTTCTGGAGACCTGACCTTTGGGGCTGTGCAGTGTTGTACTGAGTTCAGACTGTTCTCTCTTTCAG
Seq C2 exon
GAGCGTGGAAGGGGAATTTGAAGGAATTGGGAAGAGAGGCAAGGCTTGTGTGCAGCTGGCTCGGATACTGCAGTACTTGGAGTGCCCTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004622:ENSGALT00000007359:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.056 A=NA C2=0.097
Domain overlap (PFAM):
C1:
PF093445=Cas_CT1975=PD(32.8=79.6),PF0259812=Methyltrn_RNA_3=PU(16.8=90.7)
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=FE(10.3=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:
CGGCACTACACGCTGAGC
R:
GAGGGCACTCCAAGTACTGCA
Band lengths:
247-807
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]