HsaINT0025489 @ hg19
Intron Retention
Gene
ENSG00000179058 | C9orf50
Description
chromosome 9 open reading frame 50 [Source:HGNC Symbol;Acc:23677]
Coordinates
chr9:132382019-132383055:-
Coord C1 exon
chr9:132382346-132383055
Coord A exon
chr9:132382110-132382345
Coord C2 exon
chr9:132382019-132382109
Length
236 bp
Sequences
Splice sites
5' ss Seq
TGAGTGAGG
5' ss Score
1.89
3' ss Seq
CTGTTTCCTCCTGGCTCCAGCAT
3' ss Score
7.25
Exon sequences
Seq C1 exon
ATTTTTCAGGTGAGGAAACAGAGGCTCTGGGAGCTCTCGCCTGAAGCCACTCGCTGTCCGCCGGGCCGGTGGCGTTCACCCCGCACCGCGCTGCCCCGCCCGGGGCACTATGGCCTGGGGCTGGACTATGCCCTCCCCACCTCAGCCGGCGCCCCCCACCCACGCGCGCTGAGGGTGCGGTGAGCTGAGTGCGGGGCCAAGCATGTTCTGGCGTCGACTTCGCCCAGGGGCCCAGGACCTGGCGCCCAAGGGGCTCCCTGGCGACGGAGACTTCCGACGCAGCAGCGACCCGCGGCTGCCCAAGCTGACCCCGCCCGCGCTCCGAGCGGCTCTGGGCGCGCGGGGCTCCGGGGACTGGAGGATCCCGGGGGGCGGCGCCGCGTGGTGGCCGGAAGGGGACGCCAAGCCCGGGGTGGGCGTCGGACGCCTCCCGCCGCGCCTGCCCGCCTTGCTCACCGCGACCCGGCGGGCCGTGCGGAAGCGGGGGCTGCTGCGGTCCCTGCTGCCGCCTCCCCTGCTGTCGGCCGGCGCGTCCCGGGAATCGGCGCCCAGGCAGCCAGGGCCTGGAGAGCGCGAGCGCCCCCGGAGGCGCGTGGCCAGGGAGGACCCCGACTTCTTGGGCGCCTTCCTAGGAGAGCTCCTCCCCAGCAGGTTCCGTGAGTTCCTGCACCAGCTCCAGGAGAAGTGCGCCGAGGAGCCGGAGCCACTGA
Seq A exon
GTGAGGCCCCGCGGGGCCCGGGGGGCGGGCCCGAGTCATTTCCGGTGGGGGGTGGTCCCTTGTGTCCCCGCACCCACCACCCCACCACCCAGGCTAGAAGGATGCTAATGTTAGCTGAGTATCTCAGAGCCCTCGCAACCCGTCCTTGAGGGCTGGTCTGCCATCACCCCGAGGCCACATGACTAGAAAGGACCGTCCCCCAGCCAAGGCTCACAACTGTTTCCTCCTGGCTCCAG
Seq C2 exon
CATCCCCAGCACCGCAACATCAAAGGGGTGTATTAGAGCACTGCCCAGGGTCTCCGCGGTGTCCCAACTGTTCATTCCTCCCAGACCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000179058-C9orf50:NM_199350:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.606 A=NA C2=0.484
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTGGAGGATCCCGGGG
R:
ATGTTGCGGTGCTGGGGAT
Band lengths:
378-614
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)