BtaINT0144240 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020975 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497]
Coordinates
chr23:7550188-7552189:+
Coord C1 exon
chr23:7550188-7550309
Coord A exon
chr23:7550310-7552035
Coord C2 exon
chr23:7552036-7552189
Length
1726 bp
Sequences
Splice sites
5' ss Seq
CCGGTATGG
5' ss Score
8.44
3' ss Seq
CTGGACCCCCACCCTGCCAGGGC
3' ss Score
4.8
Exon sequences
Seq C1 exon
CAAGGCTTCCTGAGCCGGAGGCTAAAAAGCTCCATCAAACGCACGAAGTCACAACCCAAACTTGACCGGACCAGCAGCTTCCGCCAGATCCTGCCTCGCTTCCGAAGTGCTGACCATGACCG
Seq A exon
GTATGGGGTCTGAAGTGGGCTGGACCAGGGTGGGATGATTTGGATGCAGAGTAGGGGGCTCTGGAGTGCCCACTGCCCATTCTGTGGGGGCTATCAGAGTGCAGAGCTTGATGGCCTCAGATTGACTGAGAGGTGTTATGGGGCAGAAGCCAGAATGGAGGGGCAGCAGGAGGTGGGGAGTGGGGGCGGGGAACGGGAGCGGCCGAAAGGGGATGAAGGTGAAGCCAAGGAGGGGCTCTCCTGGCTGGGGAAGGATGGTCTCCAGGCTGGGATGGACGGAGCTGCACAGAAGGACAGAGATGGAGTGACAGCCCGGGAGAGGACAGGGAAGGGGTGGTGGGCTGGGAGGGACTGGGGGATCTGGGTGGAGGGTCCCAGGGAAGGGGGGGCGGGGTGGGGCGGGGCGGCACGTGCATGTGGAGCGTGTGGAGGAGGGCAGGCAGCACAGGTGTGCAGGTCCACAGCCCGGGGAGTGGGGGGGCGGGGGGGGGGGGAGGCTGGAGGGTTCATCACGGACTGAGCCTGAGGAGGAAGGCCGCAGACAGGCCAGAGGGCACCGTCGCCAGGGCTGGGCTGGAAGGAAACGTCGTTTGCTCCTGGGCTCCTGGGGTCTGCTTCTTGGGGTCCCTCTTTGGGATCCCCCCTCACCCGGTTCCTCCCAGGGGAGAAACCTGTCCTTCCTTCCCCCCGTCTGGCCGCCCCCGAGGCAGGGCAGGTAGGGAGTTGGGCTAGGTGAGTCACACCTTCCCCTCCCCCTCCGTGTCCCCGGAGCTGGATTTGGGGCCGGCAGGGGGTGAGGGCCTGGTATTCCTGGCCGCGGGGGCGGGGGGCCGGGGGAGCGTCGCGCTGACGGCAATGGAGCCCAAGATGACGGGGCTGCTATAAATAGCTCCACGGAGGCTCCCACACCCGAGCTCCCCCTCCCTTCCCCACTGCTCTCTACTCCTCAGCCCCTTGCTGGCTCCCAGAGCTTGGGTCCTGTGACTCCGGCCTCCACTCCCCTCAGCGCGTGGGCCTCTGCTCTCCTGAGGGGTGCTCCCAAGTTCCCCCCTGCTTGCCCTCTGTGCCCTCAGCCCGCGCTGCAGGGCCCCTGCTCACCTTCTGCCGCCCTGTCTCCACTCTTCCCTTTCCCTCTTCGTCTTCTCCTTTCCCCATCTCTTCCTCCCTAGTCCTCGTTTCCAGACCCATGCTCCTGCTCTCAGTTTTCTGCCCACAGCCTTCTCGCGTTTCTTACTATTTTCCCTCATTCGTTCCCTCAGTTTTGCTAAAATGTGTTCTCTTACCTCATTCATTCTTGGATTTATTAAGTGGTTTTTAGGTCATACCTATGTGGCAGGCCCAGACCAACATCTTCGTACTTGTAACGTTGACTCCCAAGAATCAAGACTCCCATAGCTGTGGGGTTTTTTAGGGGGGTGATCACCTAGAAGTCCCATCTAGAACTGTCCAAAGCCCACCTGTTTACTTTTTTCATTTCTGGCTTGAGATACTTCTGGGTGTCCCCAGTATTCAGAACCCCTTAGGTGGTGGACTGAGGGGAGGGGCTTTGTCTCACACCCCTTGTGTCCTTCCCTGTACGGGCTGGGTTTCTGTGTCTGTGGGAAGTGGGTGTAGGAGCGCTTTCCCCAGGTCTCTGTCCCTCCTAGAGCCTGCTTGGTGATGCAGCCGTCTGGGTTTGTAAGCAGGCTGGGCCCTGATCCCCCCTCCTGGACCCCCACCCTGCCAG
Seq C2 exon
GGCCCGGCTGATGCAGAGCTTTAAGGAGTCGCACTCTCACGAGTCCCTGCTGAGTCCTAGTAGCGCGGCCGAGGCCTTGGAGCTCAACTTGGATGAAGACTCCATTATCAAGCCAGTGCACAGCTCCATTCTGGGCCAGGAGTTCTGTTTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020975:ENSBTAT00000027936:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.341 A=NA C2=0.231
Domain overlap (PFAM):
C1:
PF0016924=PH=FE(18.0=100)
A:
NA
C2:
PF0016924=PH=FE(23.0=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:
CCGGAGGCTAAAAAGCTCCAT
R:
CAGAACTCCTGGCCCAGAATG
Band lengths:
255-1981
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]