MmuINT1032589 @ mm10
Intron Retention
Gene
ENSMUSG00000067629 | Syngap1
Description
synaptic Ras GTPase activating protein 1 homolog (rat) [Source:MGI Symbol;Acc:MGI:3039785]
Coordinates
chr17:26961436-26963087:+
Coord C1 exon
chr17:26961436-26962498
Coord A exon
chr17:26962499-26962913
Coord C2 exon
chr17:26962914-26963087
Length
415 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CCCTTCCTCGCTGGTCTCAGCAT
3' ss Score
6.06
Exon sequences
Seq C1 exon
CTCTATGGACATGGCTCGCCTCCCCTCCCCAACCAAGGAAAAACCACCACCACCACCACCCGGTGGGGGTAAAGACCTTTTCTATGTGAGCCGGCCACCACTGGCCCGGTCCTCCCCAGCATACTGCACGAGCAGCTCGGACATCACAGAGCCAGAGCAGAAGATGCTGAGTGTCAACAAGAGTGTGTCCATGCTGGACCTTCAGGGCGACGGGCCTGGAGGTCGCCTTAACAGTAGCAGTGTTTCCAACCTGGCAGCTGTTGGGGACTTGTTGCATTCCAGCCAGGCCTCGCTGACAGCAGCTTTGGGGTTGCGGCCTGCACCTGCCGGGCGCCTCTCCCAGGGGAGTGGCTCTTCCATCACAGCAGCTGGCATGCGCCTCAGCCAGATGGGGGTCACTACAGATGGTGTCCCCGCCCAGCAACTGCGCATCCCCCTTTCCTTCCAGAACCCTCTCTTCCATATGGCTGCTGATGGGCCAGGGCCCCCAGCAGGCCATGGAGGGAGCAGTGGTCATGGTCCACCTTCCTCCCATCACCACCACCACCACCATCACCACCACCGAGGGGGAGAACCCCCAGGGGACACTTTTGCCCCATTCCATGGCTATAGCAAGAGCGAGGACCTCTCTTCAGGGGTCCCTAAGCCCCCCGCCGCCTCCATCCTTCACAGCCACAGCTACAGCGACGAGTTTGGACCCTCTGGCACTGATTTTACCCGCCGGCAGCTCTCGCTTCAGGACAGTCTACAGCACATGCTCTCCCCTCCCCAGATTACCATCGGTCCCCAGAGGCCAGCTCCCTCAGGGCCGGGAGGGGGCAGCGGCGGGGGCAGCGGTGGGGGCCAGCCACCCCCCTTGCAGAGGGGCAAGTCTCAACAGTTGACAGTGAGTGCCGCCCAGAAACCTCGGCCGTCTAGCGGGAACCTGTTGCAGTCCCCGGAGCCAAGCTACGGACCTGCCCGTCCTCGGCAGCAGAGCCTCAGCAAAGAGGGCAGCATTGGGGGCAGCGGGGGCAGCGGGGGCGGAGGGGGTGGGGGGCTCAAGCCCTCCATCACCAAGCAG
Seq A exon
GTAGGTGAGGGCAGGGTGAGGTGGGGCGGGTGACAAGCAGGGAGGGAAGCAACAGTGTAGTCTGGTGTGACAAGTCTCCTTCTTTGTGGCCGGTAGTCCCACCACTCAAGAGGCAAGATGGAAGGAAGCTAGGGCTAGGTAGTGAAATTGTCTCTAAACAAACAAAAATCTCACAAACATAAGAGGGCCCTCAGCAATGTCCCATGAAGTGTTGAAGTACCAAGGATGTGTAGATGAACAGTTGAGGACCCCAGCCTTAGCACTTCATCCAGGCAGGCAGCATAACTTCACTAGTTCAGACAGAAAAGGGCTAAGGCAGGGGAGCAGGTGTGGGGGGATCATTTGTGTTTTCTTCCTCTGAGCACGCCCTCCCTCTCCCACCTTTCTGCTGTCTGCCCTTCCTCGCTGGTCTCAG
Seq C2 exon
CATTCCCAGACTCCATCCACGCTTAACCCCACAATGCCAGCCTCGGAGCGGACCGTAGCCTGGGTCTCCAACATGCCTCACCTGTCGGCTGACATCGAGAGTGCACACATCGAGCGAGAAGAGTACAAGCTCAAGGAGTACTCCAAGTCCATGGACGAAAGCCGGCTGGACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067629:ENSMUST00000194598:15
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=0.945
Domain overlap (PFAM):
C1:
PF120043=DUF3498=PD(22.2=75.0)
A:
NA
C2:
PF120043=DUF3498=FE(29.0=100),PF071957=FliD_C=PU(38.7=49.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCCCCTCCCCAGATTACC
R:
CATTGTGGGGTTAAGCGTGGA
Band lengths:
342-757
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types