Special

MmuEX6099595 @ mm9

Exon Skipping

Gene
ENSMUSG00000015087 | B230208H17Rik
Description
RIKEN cDNA B230208H17 gene [Source:MGI Symbol;Acc:MGI:2442633]
Coordinates
chr2:25440296-25441353:-
Coord C1 exon
chr2:25441144-25441353
Coord A exon
chr2:25440828-25441056
Coord C2 exon
chr2:25440296-25440464
Length
229 bp
Sequences
Splice sites
3' ss Seq
ACATTTCTTCTTATGTGAAGGTC
3' ss Score
5.92
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
Exon sequences
Seq C1 exon
TGACGATGGGGAGGCCCTAGGAGGGAACCCAATGGTGGCAGGTTTCCAGGATGATGTGGACATAGAAGACCAGACACATGGCAAATCCCTGCTGCCCTCGGATCCCATGCCCAGTAAGAACATCAGTCTCTCAAGTGAGGAGGAAGCCGAAGGACTGGCAGGCCACCCTAGAGTGGCCCCTCAGCAATGCTCAGAGCCTGAGACTAAATG
Seq A exon
GTCCTCCACCAAGGTCTCACATCCACAAAAGAAGAGAGCTCCCACGAGAGGCACGCCACCGTGGTCAGATGGTCTCACCACTGATGACTCTGAAAGACCCCAGGAAGGGAAGGACAAACAGGTGTCATCAGAGAGTGATCCTGAGGGGCCCATTGCTGCCCAGATGCTGTCCTTCGTCATGGATGACCCAGACTTTGAAAGTGATGAATCAGATACACAGAGGAGAATG
Seq C2 exon
GGCAGGTTTCCAGTAAGAGAAGACCTCTCTGATGTAACTGATGAGGACACTGGCCCTGCTCAGCCACCTCCACCTTCCAAGCTCCCAGGTGCTTTCAGACTGAAGAATGACTCCGATCTCTTTGGGCTGGGCCTAGAGGAGATGGGACCTAAGGAAAGCAGTGACGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015087-'16-20,'16-17,17-20=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact

ORF disruption upon sequence exclusion

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 Inclusion Isoform:


Main Skipping Isoform:
NA


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAGGTTTCCAGGATGATGT
R:
AGCCCAAAGAGATCGGAGTCA
Band lengths:
302-531
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]