GgaINT0125643 @ galGal3
Intron Retention
Gene
ENSGALG00000004622 | C9orf114
Description
NA
Coordinates
chr17:5908517-5909389:-
Coord C1 exon
chr17:5909291-5909389
Coord A exon
chr17:5908620-5909290
Coord C2 exon
chr17:5908517-5908619
Length
671 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
ATTCTGTGTTTGTTTGCCAGGCG
3' ss Score
8.38
Exon sequences
Seq C1 exon
AAACTAAAGTACGAAAAGGCACTGTGGTGTCTTCGCACCACCCTCGCACGGTGTCCGGTTTGTACTGGGGTTACAGCGTCCGCCTTGCCTCCTGCCTGA
Seq A exon
GTAAGTACCCAGAGGGGTTCTTTGCTTTTTACTGTGTGGAACGATCTTAATCCCAACTTGGGCTTCCACACCAATCTCAGGCCTACTGGGTACACTTCTGCTGCTTAAAATTCTCATTTTGTCTCAAAATGGGTGACCGCCAGCCAGTGATGCAGCTAGCAGTCATGCTGCTCAAATCTGAGTGCTCAAACTACAAGTGTTGAGTTGCCCCATTCATCCTCCAGTACTCTGCCCTCTACCTCCACATTACCACAGCTCTAAACATCCGTGTTGTGGCAACACAGACAAGAGTTGGTTATCTCCATCTCCATTTCTGTGATAACTACCTCCCACTTGTCCACATCAAAGCCCACGGAGACATCAGAGCTCAAAAGCCCTGCAAAATTCTTTCCCACTGTCTTCTGATAGAAGAAAAATCATAAGCCATTCATCAAGGAATGGTTCTTGGTACCTGCTGAGCTTTGAGGTGCTGCAGTTGAGTGCCAGGAGACTTCTGCAGCAATGGAATTAAGTAGGGAAAGGGATAATTCTTCATTTAGAAGGTGCATTAGTGGCACTGGGAAGCAATCACTTCTGCTGCTACCACTCACCTTTGAAGCGTCTGGACTGCCCAGAAGGCAGCATGGGTGAGAGCACCACTATGATAACCACATTCTGTGTTTGTTTGCCAG
Seq C2 exon
GCGCTGTCTTTTCAGAATGTCCGTTTAAGGAAGGCTATGATGTCTCTATTGGGACCTCAGAGCGGGGTAACTCCGTGGACCAGGTCACCCTCCCCTCCTTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004622:ENSGALT00000007359:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.324 A=NA C2=0.029
Domain overlap (PFAM):
C1:
PF0259812=Methyltrn_RNA_3=FE(11.3=100)
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAAAGTACGAAAAGGCACTGTGGT
R:
CTAAAGGAGGGGAGGGTGAC
Band lengths:
198-869
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]