GgaEX1002147 @ galGal3
Exon Skipping
Gene
ENSGALG00000008984 | C9orf86
Description
NA
Coordinates
chr17:970086-976201:-
Coord C1 exon
chr17:976072-976201
Coord A exon
chr17:970914-971132
Coord C2 exon
chr17:970086-970203
Length
219 bp
Sequences
Splice sites
3' ss Seq
AATCATTGTCTACTTTGCAGTGA
3' ss Score
5.11
5' ss Seq
AAGGTATGA
5' ss Score
9.11
Exon sequences
Seq C1 exon
CCCCTGCAAAAGTACAGAGCGTGGAGGACTTTGTTCCTGATGACAGCCTGGATCACAGCTTTTTAGAAGACTCAGCCCCACAGAAGGATAAGGGGAGACCACAGACAAAGCACCGTGTTGATAGTGAAAG
Seq A exon
TGATGGAGAGACACCTGGGGGGAACCCCATGGTGGCGGGTTTCCAAGACGACCTTGACCTGGATGACAAAATCCCCAGCAGAGCTGTGCTGGCAACAGAGCGGGTGCCCAGCAAGAACATTACACTGTCCAGTGAGGAGGAGGAGGAGGAAGAGGCTAAGGACTCTAGGGTCACACTCATACCTGATGAAAGCATTGACACGGAACGTGAAAAAAAAAG
Seq C2 exon
GTCTTCCAGAAATTCTGTGAAACCACAAAGTGAAGCAGTTCTGACCAAAGCAACTGACCCGAAGCCTCCAGACAGTTTACCTCCACATTCTGGGTCTGAAAGAAGCAGCAGCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008984-'19-24,'19-23,21-24=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=1.000 C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
NO

Main Skipping Isoform:
NA

Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTGCAAAAGTACAGAGCGT
R:
CTTGCTGCTGCTGCTTCTTTC
Band lengths:
247-466
Functional annotations
There are 1 annotated functions for this event
PMID: 19433581
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]