HsaINT0012975 @ hg19
Intron Retention
Gene
ENSG00000099889 | ARVCF
Description
armadillo repeat gene deleted in velocardiofacial syndrome [Source:HGNC Symbol;Acc:728]
Coordinates
chr22:19966420-19967765:-
Coord C1 exon
chr22:19967266-19967765
Coord A exon
chr22:19966604-19967265
Coord C2 exon
chr22:19966420-19966603
Length
662 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TGGCCAATCGCACCCCACAGGCA
3' ss Score
5.56
Exon sequences
Seq C1 exon
GGCCTACGAGGACACAGCAGATGATGGCGGCGAGCTGGCGGACGAGCGGCCTGCGTTCCCAATGGTGACGGCGCCCCTGGCCCAGCCTGAACGGGGCAGCATGGGCAGCCTGGACCGGCTGGTGCGGCGCTCGCCCTCAGTGGATAGCGCCCGCAAGGAGCCGCGCTGGCGGGACCCTGAGCTGCCTGAGGTGCTGGCCATGCTGCGGCACCCCGTGGACCCCGTGAAGGCCAATGCGGCCGCCTACCTGCAGCATCTGTGCTTTGAGAACGAGGGTGTCAAGCGGCGTGTACGGCAGTTGCGGGGGCTGCCGCTGCTTGTGGCACTGCTGGACCACCCGCGGGCTGAGGTGCGGCGCCGGGCCTGTGGGGCACTGCGCAACCTCTCCTATGGCCGCGACACTGACAACAAGGCCGCCATCCGGGACTGCGGTGGTGTGCCTGCCCTGGTGCGCCTGCTGAGGGCTGCCCGGGACAACGAGGTCCGTGAGCTTGTCACTG
Seq A exon
GTGAGTGGGACCTGGCCATGCTCACATCCCCTGGGAAGAGAAGAGTGTGAGGCTCAACCCGGGAGGAACGAGGCCACTCGGCCTGCGACCGCCTGGGAAAGCACCCGGTAGGCAGGAGTGCAGCTGCTGAGACGCTTGCCCCAGGAGCCAGGCATCAGGCCCAGACACTGTGACAGGTTCCCCAGTCTCTACCATAGCAGGGAGGCTGACGCTGCGCCCCTCGGGCATGTCCCCTCACCTCCTGCCTTCACACCTCCTGCCCCCACAGAAACTCTCCTGGGACCCACCTCCTTGGTTCCCACCCCAACCGTGCAGTGGTGGGGCTTGTGCCTTGTGAGAGCTGAGGGACAGGTAGGGTCACCGTGTCTCTGTGAGGCCCTGTGGCCTCAGGAGTGTTAGTGCCACCTGCCACATGGCAGGGAATGGGTGGGACGGGACAGCACTGCCACACCCTCCTCTGCACCTCCTCCCCTTTGGGGCTCCTTCCTAGCTGGAAACCAGTACTGGGTGTCCCCCGGAACCACTCACGGCTTTTGTTACTTCCTACTGTTCTGCATGAGCTGGGACATGAGGAGAGTGGGACAGGTCCTGAGCGTGGCCACCTGGGGAGGTAGGCAGGCGGTGCATATGGTCAGCACAGATTGGCCAATCGCACCCCACAG
Seq C2 exon
GCACCCTGTGGAACCTGTCATCCTATGAGCCCCTGAAGATGGTCATCATTGACCATGGCCTGCAGACGCTGACCCACGAGGTGATCGTGCCCCACTCAGGATGGGAGCGTGAGCCCAACGAGGACTCCAAGCCACGGGACGCCGAGTGGACAACTGTCTTCAAGAACACGTCGGGCTGCCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000099889-ARVCF:NM_001670:6
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.405 A=NA C2=0.331
Domain overlap (PFAM):
C1:
PF0051418=Arm=WD(100=24.4),PF0051418=Arm=PU(81.0=20.2)
A:
NA
C2:
PF0051418=Arm=PD(16.7=11.3)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCTTTGAGAACGAGGGTGT
R:
CTCACGCTCCCATCCTGAGT
Band lengths:
355-1017
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)