MmuINT1032595 @ mm10
Intron Retention
Gene
ENSMUSG00000067629 | Syngap1
Description
synaptic Ras GTPase activating protein 1 homolog (rat) [Source:MGI Symbol;Acc:MGI:3039785]
Coordinates
chr17:26952562-26953151:+
Coord C1 exon
chr17:26952562-26952653
Coord A exon
chr17:26952654-26953029
Coord C2 exon
chr17:26953030-26953151
Length
376 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TATTCCCATTTGCTCCCCAGCAA
3' ss Score
5.98
Exon sequences
Seq C1 exon
AATACCACTTGGGTCGCTCGAGGAGGAAGAGTGTCCCAGGGGGGAAACAGTACAGCATGGAGGCCGCCCCCGCTGCGCCCTTCCGGCCCTCG
Seq A exon
GTGAGTGAATGAATGCCAGTGCCTGCCAGATGTGGCTCAGCCTGACCCTATCTCTCCCAGCCCCAGCTGGAGCCCCATGGTTCTGAAAGAGAGGACCAAGGAAGAGTGTGCATGCATCCCCACCTCTTTGGTTTACCCCTTCTTGGCTCTGCCCCCTACTTCTTGGACCAGCCCTCCCACCTTTTCCAGCTAGTTTGTGTGTTTGTGTATCTGCTCACATCATACAGCACCCGTGGGAGCAAGGAAGACAAACTGGTGTCAGGGCTCCTGTCCCCTTTCCTCTTCTCCATGTTCTTCCAGGGATTCCTTGCCAGCTGAGGGTGTCCAGGGAGACTCTGAGCCGCCCCAGTCACCCCTATTCCCATTTGCTCCCCAG
Seq C2 exon
CAAGGCTTCCTGAGCCGGAGGCTAAAAAGCTCTATCAAACGTACAAAGTCACAACCCAAACTTGACCGGACCAGCAGCTTTCGACAGATCCTGCCTCGCTTCCGAAGTGCTGACCATGACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067629:ENSMUST00000194598:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.779 A=NA C2=0.383
Domain overlap (PFAM):
C1:
PF0016924=PH=FE(13.5=100)
A:
NA
C2:
PF0016924=PH=PU(24.8=65.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTGGGTCGCTCGAGGAG
R:
GTCATGGTCAGCACTTCGGAA
Band lengths:
206-582
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