HsaALTD0001096-1/2 @ hg19
Alternative 5'ss
Gene
ENSG00000196642 | C9orf86
Description
chromosome 9 open reading frame 86 [Source:HGNC Symbol;Acc:24703]
Coordinates
chr9:139731798-139732467:+
Coord C1 exon
chr9:139731798-139732067
Coord A exon
NA
Coord C2 exon
chr9:139732314-139732467
Length
0 bp
Sequences
Splice sites
5' ss Seq
TAGGCTGTT
5' ss Score
-9.66
3' ss Seq
CCCGGCATCACTGTTCACAGAGC
3' ss Score
4.96
Exon sequences
Seq C1 exon
CTTCCTGGAGATGATGGAGGCTCGCAGCCGTGGCCATGCGTCCCCACTGGCGGCCAACGGGCAGAGCCCATCCCCGGGCTCCCAGTCACCAGTGGTGCCTGCAGGCGCTGTGTCCACGGGGAGCTCCAGCCCCGGCACACCCCAGCCCGCCCCACAGCTGCCCCTCAATGCCGCCCCACCATCCTCTGTGCCCCCTGTACCACCCTCAGAGGCCCTGCCCCCACCTGCGTGCCCCTCAGCCCCCGCCCCACGGCGCAGCATCATCTCTAG
Seq A exon
NA
Seq C2 exon
AGCCAGTCCCGGCCGCAGAGGGCCCAGCAACGGTCCAGAGTGTGGAGGACTTTGTTCCTGACGACCGCCTGGACCGCAGCTTCCTGGAAGACACAACCCCCGCCAGGGACGAGAAGAAGGTGGGGGCCAAGGCTGCCCAGCAGGACAGCGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196642-22-24,24-24-1/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence exclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.911 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0465211=DUF605=FE(11.9=100)


Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCCTCTGTGCCCCCTGTAC
R:
AAGTCCTCCACACTCTGGACC
Band lengths:
142-189
Functional annotations
There are 1 annotated functions for this event
PMID: 19433581
This event
All four RBEL1 isoforms (A, B, C, and D) have identical N termini harboring the Rab-like GTPase domains but contain variable C termini. Although all isoforms can be detected in both cytoplasm and nucleus, RBEL1A is predominantly cytoplasmic, whereas RBEL1B is mostly nuclear. RBEL1C and -D, by contrast, are evenly distributed between the cytoplasm and nucleus. Furthermore, all four RBEL1 proteins are also capable of associating with cellular membrane. The RBEL1 proteins also exhibit a unique nucleotide-binding potential and, whereas the larger A and B isoforms are mainly GTP-bound, the smaller C and D variants bind to both GTP and GDP. Furthermore, a regulatory region at amino acid position 236-302 immediately adjacent to the GTP-binding domain is important for GTP-binding potential of RBEL1A, because deletion of this region converts RBEL1A from predominantly GTP-bound to GDP-bound. RBEL1 knockdown via RNA interference results in marked cell growth suppression, which is associated with morphological and biochemical features of apoptosis as well as inhibition of extracellular signal-regulated kinase phosphorylation. Notes: C and D: internal APA, the difference is HsaINT0025589 (retained in D). B: ALTD (ex 9, HsaALTD0001096) top ALTA (ex 15, not in VastDB) skipping exons 10 (not in VastDB), 11 (HsaEX1030457), 12 (HsaEX7005708), 13 (HsaEX6064086), 14 (HsaEX6064085).
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)