BtaINT0144228 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020975 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497]
Coordinates
chr23:7554988-7556853:+
Coord C1 exon
chr23:7554988-7555132
Coord A exon
chr23:7555133-7556616
Coord C2 exon
chr23:7556617-7556853
Length
1484 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
3' ss Seq
TCCCCGCCCCTCCCCGCCAGCGT
3' ss Score
8
Exon sequences
Seq C1 exon
GGGAATTCATCCGTGCTCTGTATGAATCTGAGGAGAACTGTGAGGTGGACCCCATCAAGTGCACGGCATCCAGTTTGGCTGAGCACCAGGCCAACCTGCGGATGTGCTGTGAGTTGGCCCTGTGCAAGGTGGTCAACTCCCATTG
Seq A exon
GTGAGACTGGGAACTCTGGGTTGGGGGGCCAGGGTTGGGGGAGTCGTGTGTTCATCTGTTCATCCATCTGTCCATCTTCAAAGAGACCCAAGAACCAGTTGTGGGCAGAGTGCTGTGCTCAGTGGTATAGAGCAGACAGAGAGCTGCGAGGCTTGGCCTCTGCCCTCAGAGGCCCTGCACCAGAGGGGGCGGGATATCAGAGATGCAGAAAGCCAAGGGGCAGTGTAGTATGTGTTAAGTTCCAAGAAGGGGACCCTCCATCCCGCCTCCACACATAAGGTCAGAGAAGGCAGAGCTTGGAGATGAGCAGAGACAGCTTCATGGGAGAGGTACTCCTGGGATGGGCTTAGAAGATTGGGCCAGGTTCTGACCTATAGAACATGGTGGGTTGAGAAGCTGCCTCCGGAGAAGGCTGTGGAGCAGACCTATGCGTGAGGGCGAGAGGTCCTGGGGCAGCAGGCAGAAGTGGTTTAGTGGAGCGTGTGGCTCACTTCAGTGGGGAATGGAGGGCCACGTGGTGGGACGGGGTGAGGAAAGTTAGCGTGTGAAGGCCTCACTGCCCAGTAAGGGAGCCTGAGTTCTCAGTAGGTCAGGGGACGCCTGTGACGGTGTGCAATATCGTGACCGTGAAGGTTAGGCCTTCAGTAGAAATGGGCGCAGAGGCGGTTGGATAGGGAGATGAAGTCCAGGCTAGTTGGGGGCAGTTGTTACTGTGTCAGGCATGGAAATCAGATCCTGAGTCAGGATCTGGCAGGAAAAGTAGAAAGGGGCCTCTGTAAGGACCCTCTGCAGAGAGGATCACCGGGTGTCCTCAGCTAATTGGAAAGGAAGGGCTGTGTCTGGGGGGGTCCTGAGGCCGTGAGGCTGGTGGCTGGGCGACCAGTGGCCTAACTGACAGAACCAGGGAGTCAAGAGGGGGAACTCAGCGGAGGTTGGAGGTGTGGGAGCAACGCTCAGCTCTACTCTCCATGGTTCGAAGTTTAAGGTGTCAATGGGACATTGCAGAGGAGGGCCTGGGAGTGGGGGGGGTTTGAACTCTGAGCTGTTCCAGGGATTGGGGCCATGCCTGGGGTGCCTCCATCCCCATTTCCCTGGAATCCAGAAGAGTTGGGGGGTCCGAGCTCCCTGTACCTCAAGTGACCCTCCATCTCTCTCCCATCTCTGTCTCTCCCGGTGTCTTCTTCTCTTCTCCTGCTCTCCTCGTCTCTCTGGCACACGCGCTGTCTCCCCGTGTGTCCCTGTCCCCCGCCTCCCCCTCCGGCCCGCTTTCCGCCGTCTGTCCCCGCCGCAGCCCTTTTCCTCCTCAGCCCCCATCCTCCCCCCACGCCCTCCCTCATGCCCTGTCACTCTCACCTCTGCCTCTGCACCCTCGCCTCCTAACACCCCCCTCAGCATGTTCCCTGGAAGCTGAGGGTCTCTGGGGCTCAGTCCCGGTCTCTCTCTCTCTCTCTCTTTCTCTCTGTCTCCCCGCCCCTCCCCGCCAG
Seq C2 exon
CGTGTTCCCGAGGGAGCTGAAGGAGGTGTTTGCGTCCTGGCGACTGCGCTGTGCAGAGCGGGGCCGAGAGGACATTGCGGACCGGCTGATCAGCGCCTCGCTCTTCCTGCGCTTCCTCTGCCCGGCCATCATGTCGCCCAGCCTCTTCGGGCTCATGCAGGAGTACCCAGATGAGCAAACTTCGAGAACCCTCACGCTCATCGCCAAGGTCATCCAGAACCTGGCCAACTTTTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020975:ENSBTAT00000027936:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon 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
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAGAACTGTGAGGTGGACC
R:
TGGAAAAGTTGGCCAGGTTCT
Band lengths:
351-1835
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]