BtaALTA0029322-2/3 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000020975 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497]
Coordinates
chr23:7554988-7556824:+
Coord C1 exon
chr23:7554988-7555132
Coord A exon
chr23:7556440-7556616
Coord C2 exon
chr23:7556617-7556824
Length
177 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
3' ss Seq
GCAGCCCTTTTCCTCCTCAGCCC
3' ss Score
6.11
Exon sequences
Seq C1 exon
GGGAATTCATCCGTGCTCTGTATGAATCTGAGGAGAACTGTGAGGTGGACCCCATCAAGTGCACGGCATCCAGTTTGGCTGAGCACCAGGCCAACCTGCGGATGTGCTGTGAGTTGGCCCTGTGCAAGGTGGTCAACTCCCATTG
Seq A exon
CCCCCATCCTCCCCCCACGCCCTCCCTCATGCCCTGTCACTCTCACCTCTGCCTCTGCACCCTCGCCTCCTAACACCCCCCTCAGCATGTTCCCTGGAAGCTGAGGGTCTCTGGGGCTCAGTCCCGGTCTCTCTCTCTCTCTCTCTTTCTCTCTGTCTCCCCGCCCCTCCCCGCCAG
Seq C2 exon
CGTGTTCCCGAGGGAGCTGAAGGAGGTGTTTGCGTCCTGGCGACTGCGCTGTGCAGAGCGGGGCCGAGAGGACATTGCGGACCGGCTGATCAGCGCCTCGCTCTTCCTGCGCTTCCTCTGCCCGGCCATCATGTCGCCCAGCCTCTTCGGGCTCATGCAGGAGTACCCAGATGAGCAAACTTCGAGAACCCTCACGCTCATCGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020975-26-16,26-15,26-14-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061614=RasGAP=FE(27.9=100)
A:
NA
C2:
PF0061614=RasGAP=PD(44.2=95.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCGGATGTGCTGTGAGTT
R:
GCGTGAGGGTTCTCGAAGTTT
Band lengths:
247-424
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development