Special

HsaEX6064085 @ hg19

Exon Skipping

Gene
ENSG00000196642 | C9orf86
Description
chromosome 9 open reading frame 86 [Source:HGNC Symbol;Acc:24703]
Coordinates
chr9:139734146-139735639:+
Coord C1 exon
chr9:139734146-139734317
Coord A exon
chr9:139734606-139734664
Coord C2 exon
chr9:139734774-139735639
Length
59 bp
Sequences
Splice sites
3' ss Seq
TGTCTGTCCTGTCTGTGCAGGTA
3' ss Score
11.63
5' ss Seq
GAGGTACTG
5' ss Score
7.67
Exon sequences
Seq C1 exon
GATGACTTTCCCGTGCGAGATGACCCCTCCGATGTGACTGACGAGGATGAGGGCCCTGCCGAGCCGCCCCCACCCCCCAAGCTCCCTCTCCCCGCCTTCAGACTGAAGAATGACTCGGACCTCTTCGGGCTGGGGCTGGAGGAGGCCGGACCCAAGGAGAGCAGTGAGGAAG
Seq A exon
GTAAGGAGGGCAAAACCCCCTCTAAGGAGAAGAAGAAGAAGAAGAAAAAAGGCAAAGAG
Seq C2 exon
GAAGAAGAAAAAGCTGCCAAGAAGAAGAGCAAACACAAGAAGAGCAAGGACAAGGAGGAGGGCAAGGAGGAGCGGCGACGGCGGCAGCAGCGGCCCCCGCGCAGCAGGGAGAGGACGGCTGCCGATGAGCTGGAGGCTTTCCTGGGGGGCGGGGCCCCGGGCGGCCGCCACCCTGGGGGTGGCGACTACGAGGAGCTCTAGGCCGGCGTGGGCAGTGGCCGCCCTGGGGCGGGGGGCGTGCCTGTCACTGCCTGGGGAGGCATTTGCCTCTGTACCATCGCCTTTGCCGCTGCCCCGTGGCTGCCGTGTGCGCTTCTGAGCTGGAAGAGGCCGGGCATTGGTGGTCCCCAGGCTGGGCCCTGCAGGTGCTGGGCCTTCAGGCCCAGTGTGAGCCTGCTCTGCAAGAAGGGAGGGGACAGCTGGCTTCAGCCAGGCTCGGTGGACACCCTGGCCCTCTCGGGGCAGAGCCGCCAGTGTTTCTCAGGGATGTGACTGAGGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196642-'29-30,'29-29,31-30=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (No Ref, Alt. Stop)

No structure available
Features
Disorder rate (Iupred):
  C1=1.000 A=1.000 C2=0.714
Domain overlap (PFAM):

C1:
NO
A:
NO
C2:
NO


Main Inclusion Isoform:


Main Skipping Isoform:


Other Inclusion Isoforms:


Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
HIGH PSI
Zebrafish
(danRer10)
HIGH PSI
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGACTCGGACCTCTTCGGG
R:
CTCCTTGCCCTCCTCCTTGTC
Band lengths:
133-192
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