BtaINT0144239 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020975 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497]
Coordinates
chr23:7549697-7550309:+
Coord C1 exon
chr23:7549697-7549788
Coord A exon
chr23:7549789-7550187
Coord C2 exon
chr23:7550188-7550309
Length
399 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
CCCCATTTCCCCCCACCCAGCAA
3' ss Score
5.05
Exon sequences
Seq C1 exon
AATACCACTTGGGTCGCTCGAGGAGGAAGAGTGTCCCAGGGGGGAAGCAGTACAGCATGGAGGCCGCCCCCGCCGCACCCTTCCGGCCCTCG
Seq A exon
GTGAGTGAAGGCCCTGCCAGATGTGGCTCAGCTGGTCCCCTCCCCGCCAGTCCCAGCTGGAGCCCCTGGACTGTGAGAAAGGGGGCAGGAGAGAGAATCTGTGCGTGTGTCCCCCCACCTCTTTGGTTCCCCCCTTCCTGGCTCTGCCCCCCCTGCTTCTCAGACCAGCCCTCCCACCTTCTCTAGGCTGGTGTGTGTGTGTGTTTGTGTGTGCACTCGCACCCGTGGGAGCAAAGGAAGACAAACTGGTAGCAGGGCTCCTGTGCCCTTTTTCTCACCCTGGAGACTTCCCTTTCCCCCAATCCCGCCTTCATCCAGGGGCTCTTTACCAGCTGAGCAGTGAGCAGGTGGAACTGACCCTACCCCAGCCCACCCCTATCCCCATTTCCCCCCACCCAG
Seq C2 exon
CAAGGCTTCCTGAGCCGGAGGCTAAAAAGCTCCATCAAACGCACGAAGTCACAACCCAAACTTGACCGGACCAGCAGCTTCCGCCAGATCCTGCCTCGCTTCCGAAGTGCTGACCATGACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020975:ENSBTAT00000027936:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.774 A=NA C2=0.341
Domain overlap (PFAM):
C1:
PF0016924=PH=FE(13.5=100)
A:
NA
C2:
PF0016924=PH=FE(18.0=100)
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:
ACTTGGGTCGCTCGAGGAG
R:
GTCATGGTCAGCACTTCGGAA
Band lengths:
206-605
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]