BtaINT0144227 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020975 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497]
Coordinates
chr23:7537952-7541285:+
Coord C1 exon
chr23:7537952-7538018
Coord A exon
chr23:7538019-7541163
Coord C2 exon
chr23:7541164-7541285
Length
3145 bp
Sequences
Splice sites
5' ss Seq
GAGGTACGG
5' ss Score
9.4
3' ss Seq
TGTGTATCTCTGCCCCCTAGATG
3' ss Score
9.62
Exon sequences
Seq C1 exon
ATGAGCAGGTCTCGCGCCTCCATCCATCGGGGGAGCATCCCCGCGATGTCCTATGCCCCCTTCAGAG
Seq A exon
GTACGGTGGTGAGGGGAGGGGGAGGACCAGTTGGGGGGGAGAAGGGGGGGAGGGGCGGGGGGGGGCTGGGCAGAACTGGGGCCAGGGAGGGGAGCAGCTGAAATGGAAGGAGAGAGGAGGACTCGGAAGGCAGGGATGGGAGCAATGGGGAAGGAGGGATTGGAGGATAGGGGTAAATAGGGACCGGAGGGGCCAAGAAACAGGCCTTGAAGGGGGCTGAGGGGGAAACGATGAAGGGAAAAGAGATCGCCAGAGAAGGTGGGAAGATAGAAGGGTAGGGTTGGGGGAAGAGCTGCAGAAATAATTTGGAGGTGGGAGCTGAGAGATGAGGAAAATATCAAGGAAATAGAATGACAGAGTCTTAGGAGAGGGACTAGGAGGGGAAAATGAAGAAAATTAAAACATAGGGGTGAAAATAGCAGCCAAGAAGATGAGGGCTAGGATCTGGTGGGGTCTCAGAGTATGGTAGGGGGTAGAAAAAGACAGGAGATGGAGGGAGAAGAGAGGGGGCCAGATGGAGAGAGAGGGAGGCAGTAGGGGGGGTGGCGGGGAATGGAGGGTCCAGATGGAGGGAAGAGAGGAGAGAGAATGGGGAATGGGTTTGGGGGAGGAGAGACCAGGGCAGGGGGAGGGCCAAATTAGGTATGTGTTTATTGGTGGGGAGGGGGGCAATACAAGTAAAACTGAGTGCTGGTAGTAGGGGCAGATTAAGACCCGGCCCCAGACTCAGGCCCTCATTAAGGCCCTTGAGCATTGAAACGTAATCCCTGGGGGCTTATCCACTTCCTTCACTTCACCACTTTCACCCCTCCCCCACCTCCAGTCCTTATTTCCATTCCCCCTCCCTCTGGTGTCCACCACCTATATCTTTCCCCACATATGGTGTCCGTTCCTTATATGAGTCCCCCTTCTGTCCTTCCCCTGTATCAGTCCCTGCTCTGGTGCCCCTTCTCTCTCTCCCTCTCTTCCGCCTGGTAGTCCTTTATATCTCTACCACCTCTCCACCCCCTCCTTCTTGGCCCCCTCGTCTTAATGTCCCTATTATGTCCCCCTCACTTCCTTTGGGCCCTTCTGGTGTATTCCCTTGTCCCTAAAGATTTACCATCATCTCTGACTCTTACTCCCTTAGATCCATTCCTGTTATTTCTTCTCCACCCCATCCCTTCTTCCCCACCCCATTCCCTATCTTATCACAAGTCTGTGCCTACTTACTTTCCCCTAAGACCCCATCTCTTATCACCCATTCCTCTTCTCTCGTCTCCTCTCCTTCCTGGGCTGTTGGAGATTTGGGGAGCAAAGACACCAGTTTTGACAGTTGGAACAGGACCTACAAGAGATCCCCATCTGAGCCCCATGGAAGTGTTCATCCTAGCAAACCTTCCCCCTTTCTTAACTGCGTCCTTCTGTCTCTTGCATCTGCCTCCCAGAATCATCCTGCGTCCAGGCAGTGTTTGTGTATGTGTGTATTCCAGAGTTGCTCCTAAGTGAAGTTCCCCGTGTCCTTCCCCACTCCCAGGAGGAGGGTGTCCCCTGAAGTCTAACTGTCCTCCCTGTGGCTGCTGTCTGACCCAGTCCCTCCTATAATGATGATGTGAATCAACAGATGTCCCCTCTGGGAGTCCTCGGGGTCTGACTGCAGTGGGCATGTTTCCTGCAGTATCTGCAGTCTCAGAGTCTCAGAGTTTTGGTGATCTCTTTATCTAAAGGGTATGTCTCTGAGGTGGCACTGACAGAGTTTCAAGAGGATTGGGGTTTTTATATACCTGTGTTCAGGGAGTTCACCTCTGTCTCTGACCTGCAGATTGGGTAAATTTGAACCATGTTTACAGACAGGGGCTAGATTTTTTAACACTCTGCTACTCATAGCTTTTAGTTGGAATGAAGTTCACTGGCCAGTTCTTTTCCTGCAATATTCCCATGATTAATTATCCTGGAAAGGTAAGGGGATTTGATCTTTTTCCTCTAAACTCTCTGTCACCCTCATTCCTTAAGCTTCTTTTCTATCACGCTGATGTCATCAATTTGATCTCTCTGACTTCTAGAGGGCCTGCCCACTATGCCGCCATGATGGTGTGTAGCACTGGGGTTTAAAGGAGAGGCACTTTGCACGCACAGGGGTGTGGAAGAACAGCAGAATCAGGGGAGGGGCGACCCTTAGTCTACTACTTGTGGAAGTTTTGTCCCCATCCCCAGCCTCTATGTCACAGGCCTGGGTCTTTCATTCTTCCCTCCCCTCTTCCTTCCTCAGGCTTCTCACGGTGCCTTGGGGAGGTTCCTACTTGAGGAGTTGGCTTCCATCCTGTCCATGGAGACTGGGGAGGTGGGATAGGGGACAGTATTGAATCTTTGACCTCTGGGCATGGAGTAGGGGAAGAGATCAACTCAGTATTCATGCAAACAAGGGCATATTTCCTGCCTCCTCAGTCCCCAACCCTTCCACAGCCAGATACCAACAAGACCCATCCTTCCTCTCCCACCAGCAGAAGCAGCTCTTTCCCTGAAGGATAAAGCAGAGTTGGGCTGGGGAGGAGGGAGTGAAGGAAAGCAGAGAGGCAGGAGAGGAGGCCCTCTCAGGATTCTGACCCTGGGAATAAGTCAGTTGCTCACTCCCTTTCTTTTCTAGACATTTAGCTTTTAGTCTCATGACCCAAATGTTCCTACATCCCCATCCTTCTTCCCATAGCTCTGTAGGCTTCCGTACTCTCTTGCAGATGGGTGGGGCCACCTTCCAAATCCTCGTCTTCTGCAGCTATCTGGTTGCCCTTCCTCTTCCCAGACACTTGCCACCAACCTTCTGGTATTTTTCTTCCGCCAGTTTTGCTGGACCCTCCGCCTTTTGACTTTTCAGAAGTGGATGGAGAGCTCCTTCCCCTTTCTCTGCCTCCAAACTCACACTCTGTCAGGATATCATTCCCCTCTGAACCACTTCTCTGTATTTTCTTCTGCCAAGTCTACTGAGCCCCTCAGCTCCCACCGCCCCAGCCAGAGAAGCTTTTCTTCTGTTCCTCTATAGTTTTCAGGGGCCTCACCCCCTTCTATGATCTCCTTAAGGTGGGTGGGGGCCCCTTGTTCCCCTTTATGGACTCTTCTGTCCCCTGAACGCATAGAGCTTCCCTTACGGTTTCTGTGTATCTCTGCCCCCTAG
Seq C2 exon
ATGTACGGGGACCCCCTATGCACCGAACCCAATACGTTCACTCCCCGTATGATCGTCCTGGTTGGAACCCTCGGTTCTGCATCATCTCGGGGAACCAGCTTCTCATGCTGGATGAGGACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020975:ENSBTAT00000027936:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.457 A=NA C2=0.366
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0016924=PH=PU(14.9=80.5)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]