BtaINT0144233 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020975 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497]
Coordinates
chr23:7558427-7560023:+
Coord C1 exon
chr23:7558427-7559504
Coord A exon
chr23:7559505-7559849
Coord C2 exon
chr23:7559850-7560023
Length
345 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
TTCCCTCTCCCCTGCCCCAGCAT
3' ss Score
7.53
Exon sequences
Seq C1 exon
CTCTATGGACATGGCTCGCCTCCCCTCCCCAACCAAGGAGAAGCCCCCGCCACCACCGCCTGGTGGGGGGAAAGACCTGTTCTATGTCAGTCGCCCACCCCTGGCCCGGTCCTCCCCCGCCTACTGCACGAGCAGCTCGGACATCACAGAGCCGGAGCAGAAGATGCTGAGTGTCAACAAGAGTGTCTCCATGCTGGACCTGCAGGGCGACGGGCCCGGCGGCCGCCTCAACAGCAGCAGCGTGTCCAACCTGGCAGCTGTTGGGGACCTGCTGCACTCGAGCCAGGCCTCCCTGACCGCGGCTTTGGGGCTGCGGCCTGCGCCTGCTGGCCGCCTCTCCCAGGGGAGCGGCTCGTCCATCACCGCGGCCGGCATGCGCCTCAGCCAGATGGGCGTCACCACAGACGGTGTCCCTGCCCAGCAACTGCGCATCCCCCTCTCCTTCCAGAATCCTCTCTTCCACATGGCCGCTGATGGGCCAGGCCCCCCAGGGGGCCACGCAGGGGGCGGCGGCCACGCCCCACCCTCCTCCCACCACCACCACCACCACCACCACCACCACCGAGGCGGAGAGCCCCCAGGGGACACCTTTGCCCCGTTCCACGGCTACAGCAAGAGCGAGGACCTCTCCTCAGGGGTCCCTAAGCCCCCTGCCGCTTCCATCCTTCACAGCCACAGCTACAGTGATGAGTTTGGACCCTCTGGCACTGACTTCACCCGTCGGCAGCTCTCACTCCAGGACAACCTGCAGCACATGCTGTCCCCTCCCCAGATCACCATTGGTCCCCAGAGGCCTGTCCCCTCAGGGCCTGCAGGCGGGAGCGGTGGTGGGGGCAGTGGTGGGGGCGGCGGGGGCCAGCCGCCCCCGTTGCAGAGGGGCAAGTCTCAGCAGTTGACAGTCAGCGCTGCCCAGAAACCTCGGCCGTCCAGTGGGAACCTGCTGCAGTCGCCAGAGCCGAGTTATGGCCCTGCCCGCCCACGGCAGCAGAGCCTCAGCAAGGAGGGCAGCATCGGGGGCGGCGGGGGCAGCGGTGGTGGTGGCGGCGGCGGGGGGCTCAAGCCCTCCATCACCAAGCAG
Seq A exon
GTAGGACGGGCGGGAGGGCTGGCAGGGCAGTGAGCGGGAGGGGAGGAGGAGGAGATGGGTCGAGGGGAGCACAACATTCTGTGGTCTGAAGTCACAGTTTTCTCACCTCCTTTCGTTCATTAAGCAAAGTGCACAGAGGGCCTGCTTTGCTCCATGTGATGTTCTGGGCACTGTGTGCTTGTCAGTTAACAGACAGGCCTCCCTGCCCTCTTGGGGCTCCCAGGGCAGATGTGATGAGAACAGCATTCATGAGGGGATCAGTCGGGGGACTCCCATTTCCTTGGGCCGTGCTCCCTGCCTTTCAAAGCGCCCACCTCCTTCCGCCTTCCCTCTCCCCTGCCCCAG
Seq C2 exon
CATTCCCAGACGCCGTCCACGCTGAACCCCACGATGCCGGCCTCCGAGCGGACGGTGGCCTGGGTCTCCAACATGCCTCACCTGTCGGCTGACATTGAGAGTGCCCACATCGAGCGGGAAGAGTACAAACTCAAGGAGTATTCCAAGTCTATGGACGAGAGCCGACTGGACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020975:ENSBTAT00000027936:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.953 A=NA C2=0.948
Domain overlap (PFAM):
C1:
PF120043=DUF3498=FE(60.0=100)
A:
NA
C2:
PF120043=DUF3498=FE(9.5=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:
CTCAGCAGTTGACAGTCAGCG
R:
CGGCTCTCGTCCATAGACTTG
Band lengths:
358-703
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]