HsaINT0021658 @ hg19
Intron Retention
Gene
ENSG00000177025 | C19orf18
Description
chromosome 19 open reading frame 18 [Source:HGNC Symbol;Acc:28642]
Coordinates
chr19:58485467-58485902:-
Coord C1 exon
chr19:58485680-58485902
Coord A exon
chr19:58485572-58485679
Coord C2 exon
chr19:58485467-58485571
Length
108 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCT
5' ss Score
6.52
3' ss Seq
CAAAAAGTTTTCTTTTCAAGGCA
3' ss Score
5.12
Exon sequences
Seq C1 exon
AGTAGAACTTCTTGATTCCTCAGATAAATAGAGGACAGATGCTGGACTGTAGCTAAGTATTTCCTTTCATCTACGGGATAAAATACTGATAATTTGAGAGTGATGGACAAGGTTCAGAGTGGTTTCCTCATTTTGTTTTTGTTTTTAATGGAATGCCAACTTCATTTATGCTTGCCGTATGCAGATGGACTCCATCCCACTGGAAACATAACAGGCTTACCAG
Seq A exon
GTAGCTTCAACCACTGGTTTTATGTGACTCAGGGAGAATTGAAAAGCTGTTTCAGGGGAGATAAAAAGAAGGTAATTACATTTCACCGCAAAAAGTTTTCTTTTCAAG
Seq C2 exon
GCAGTAAACGGTCACAACCACCCAGAAACATCACCAAAGAGCCCAAAGTGTTCTTTCATAAAACCCAGTTGCCTGGGATTCAAGGGGCTGCCTCGAGATCCACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000177025-C19orf18:NM_152474:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.122 A=NA C2=0.458
Domain overlap (PFAM):
C1:
PF097165=ETRAMP=PU(29.7=92.7),PF111393=DUF2910=PU(7.1=19.5)
A:
NA
C2:
PF097165=ETRAMP=FE(27.3=100),PF111393=DUF2910=FE(31.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
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:
GGACAGATGCTGGACTGTAGC
R:
ACACTTTGGGCTCTTTGGTGA
Band lengths:
242-350
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
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)