HsaINT0012974 @ hg19
Intron Retention
Gene
ENSG00000099889 | ARVCF
Description
armadillo repeat gene deleted in velocardiofacial syndrome [Source:HGNC Symbol;Acc:728]
Coordinates
chr22:19967266-19969260:-
Coord C1 exon
chr22:19968734-19969260
Coord A exon
chr22:19967766-19968733
Coord C2 exon
chr22:19967266-19967765
Length
968 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CGCCCCACTTGCCTGTGCAGGGC
3' ss Score
8.98
Exon sequences
Seq C1 exon
GTCACCAAGACTGTCAAGACGGTGACCACTCGGACAGTACGCCAGGTGCCCGTGGGCCCAGATGGACTCCCCCTGCTGGATGGCGGCCCCCCACTAGGCCCTTTTGCAGATGGTGCCCTGGACCGGCATTTCCTGCTGCGTGGTGGTGGCCCAGTGGCCACACTCTCTCGAGCCTACCTCAGCAGTGGGGGTGGCTTTCCCGAAGGCCCCGAGCCCCGGGACAGCCCCAGCTATGGCAGCCTGTCCCGAGGGCTGGGCATGCGGCCCCCACGTGCTGGCCCCCTTGGCCCAGGCCCTGGTGATGGCTGCTTCACACTGCCTGGCCACCGGGAAGCCTTCCCGGTGGGTCCTGAGCCTGGGCCACCAGGTGGCCGCTCCCTGCCCGAGCGCTTCCAGGCAGAGCCGTATGGCTTGGAGGATGACACGCGCAGCCTGGCCGCTGATGACGAGGGTGGCCCTGAGCTGGAGCCTGACTATGGCACGGCCACAAGGAGGAGGCCTGAGTGTGGGCGGGGCCTTCATACCAG
Seq A exon
GTGAGCTGCACCCCGTCCCCTGTGGCTACCTCCTCTGGGAAGTCTGCCCTCCACCCCCCAACTACAGAGTGCCCCACTTGTCAAGTGGCGCAGTTGAGTTAGTCATGCATGTTAGTTTGAATTGGCCTTGGCTCTCGTCAGGGACAGAAGAAAGGTGGACCCTGGGGTGGTAGGAGTTCGGCTGGGCACTGTCCTGCAGGCCCAGGGCCCAGGAAAGCTGGGAAGAGTGCCGGCCACTGGCCTTGCTCCAGCCACACTCTGGGTAACCAGAACCCAGAGCCCTGGCCCTTGTCACAGCCCCTGGTTCTGTCCCCATTGCCCTCAGTTTCTGCATCTCTGGAGTGGGGATGTGACCACAGCCCGGGTCAGGATTTTGTTGTGTGACCCTGGCCAAGTCACCTGACCGTCACTCCTAGCCTCAGGGCAGGCGGTTTGATGACAGCAACCCACAGGGCTACTGAGAGCTAAGGAGATCTTGTGCCCCAAGGGGCTGGTGGCCTGAATACTCCTCAGGTGGTCCTACTGGGATGGCTTCATGCGGAGAGGGCCATTTACTCCCCCTACATCCTGGCACAGCCAGAGATGGGCCTCATGGAAGATGGGGTGGTTTTGTGGAAGGGAGGTGAGACGGTCTCTCCAGCAGCCATAGCAGATGTCTCACAGAAACTTGTTTTGCTCGGGATTGGGAAACTGCCCGGTGACAGCAGTGAGTGAGTTTGCTGTCCTGGGAGGGTTGCCTGGGTCCTGGTAGCCGCTGGCTGGGGTTTGGCATTTGGCTCTGAATTGGTTCTCACTGGGCTGGTGCATGACTCTCTGTGTCCCCACCATGCTCCGGGCCAAGATACAGGTGCTCTCAGCCCAGCGCTGCTGGGTGAGTTTGCAGTCCTGAAGAAGGTGTGATGGGGCAGCTCAGAGGCAGGGCTGGCGGCTGCTGTGACGATGTCCACGCGCCCCACTTGCCTGTGCAG
Seq C2 exon
GGCCTACGAGGACACAGCAGATGATGGCGGCGAGCTGGCGGACGAGCGGCCTGCGTTCCCAATGGTGACGGCGCCCCTGGCCCAGCCTGAACGGGGCAGCATGGGCAGCCTGGACCGGCTGGTGCGGCGCTCGCCCTCAGTGGATAGCGCCCGCAAGGAGCCGCGCTGGCGGGACCCTGAGCTGCCTGAGGTGCTGGCCATGCTGCGGCACCCCGTGGACCCCGTGAAGGCCAATGCGGCCGCCTACCTGCAGCATCTGTGCTTTGAGAACGAGGGTGTCAAGCGGCGTGTACGGCAGTTGCGGGGGCTGCCGCTGCTTGTGGCACTGCTGGACCACCCGCGGGCTGAGGTGCGGCGCCGGGCCTGTGGGGCACTGCGCAACCTCTCCTATGGCCGCGACACTGACAACAAGGCCGCCATCCGGGACTGCGGTGGTGTGCCTGCCCTGGTGCGCCTGCTGAGGGCTGCCCGGGACAACGAGGTCCGTGAGCTTGTCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000099889-ARVCF:NM_001670:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.960 A=NA C2=0.405
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0051418=Arm=WD(100=24.4),PF0051418=Arm=PU(81.0=20.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGAGCTGGAGCCTGACTAT
R:
ACACCCTCGTTCTCAAAGCAC
Band lengths:
350-1318
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)