MmuINT1032584 @ mm10
Intron Retention
Gene
ENSMUSG00000067629 | Syngap1
Description
synaptic Ras GTPase activating protein 1 homolog (rat) [Source:MGI Symbol;Acc:MGI:3039785]
Coordinates
chr17:26958077-26959845:+
Coord C1 exon
chr17:26958077-26958221
Coord A exon
chr17:26958222-26959608
Coord C2 exon
chr17:26959609-26959845
Length
1387 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
3' ss Seq
TCCCCACCCCTTCCCCCCAGCGT
3' ss Score
9.36
Exon sequences
Seq C1 exon
GGGAGTTCATTCGTGCTCTGTATGAATCTGAGGAGAACTGTGAAGTAGACCCCATCAAGTGCACAGCGTCCAGTCTGGCAGAGCACCAGGCCAACCTGCGGATGTGCTGTGAGTTGGCCCTGTGCAAGGTGGTCAACTCCCATTG
Seq A exon
GTGAGACTGGGAACGCTGGGCTGGGGGGCCAGGGCTGGGCAGTTGTGTGTTCATCTGTTCATCCATCTGTCCATCCTCAGAGGACTGAGCATCAGTACGGGCAAAGCATTTTCTGGGGTATCATAGAACAAAGAGGTGAATGAGGGCTGCTTCCTGACCTCAGATGGCCTCTAACCAAAGTGAGCAGGGACACACGAGATGCAAGAAAAGCCACAGAGCCATTATGATGTGTGTTAAGGGAGGGCCCCTGGGTAGATAGAGCAGTGATGAGGTGCCCAGGGCTGGGCTGTGAGGACCGGCTCAGGAGCTGGCATCTGTACACAGTAGGCAAAGGACATTTCCAGGGCCGTGAGATAGCACAGGTGTGATGTGAGGAGGCCTTTGAGCTTCAGAGGATGGCTGGCAGCTGGTGCACATGGCTCTAGTGGAGGCAATAGGAGAGAGCTGTGCTTTGGGAATGAGAGAATCTGGAAGTCCAGGGCTCAGGAGTCTGCAACTGTCAAAATGCTTTGGGGTAGCTTTGAAGGAGTTGGTACCAGGAGGAAGCATGACTGAGACTGGCTCACAAGTCAGTGAGCTATATGGGGAGGGAGAGAAAGCAGCCCAGACCATTGGAGGCTCTGGTCCAGGTGTGGAAACCAGATGTTGGATCAGGGTGTAGTTAGAAGGCCTAGAAAGGGTCTGCTCAAGACCAGCTAGAGGAAGGATCAAATCAGTAGGGGTCGTCTGAGGGGTTGTGTGGGAGTCAGGATGACTCAAGAGGTCATGAGACTGCAGTGCTTAGGAGACCCACAGCCTCATTGACAGAACCAGGGAGTCAGAAGGAGGAGCCAGCTGGCAGTGTGGGGGCGATGGTGAGCTCTGTTTTACACTAGTCAAGTTTAAGGTGTCAGTGGGACATGGAAGTAGCACTGGGAGGCGGGAAAGAGTGAGCTGAGCCATTCCAGGGACTGGGGATCATGCCTGGGGCACGTCCATCCCCATTTCCCTGGAATCCAGAAGAGTTGGGGGGTCCGAGCTCCCTGTACCTCAAGTGACCCTCCATCTCTCTCCCATCTCTGTCTCTTCCCTGGTGTCTGTTTTTCTTCTCCTCCTTTCCTTGTCTCTCTCCCACCCTCCGTCTCTCTCCCACGTGTCTATCTCCCCTCACCCCTCTCCCCCTCTCCATTTCTCTCTCCAGAATCTGTTCCTCTACTGTGGCCCTCTTCTTCAGCAGCCTCCTGTCTTTCTCCTGCAGTCCCTCCCTCCCGGTCTCTCTCACCTGTCTCCACACCCTCACCTTCTACCACCCCCTCAGCATGTTCCCTGAAAGCTGAGGGTCTCTGGGGCTCAGTCCCGGTCTCTCTTTCTCTCTTTCTCTCTCTGTCTCCCCACCCCTTCCCCCCAG
Seq C2 exon
CGTGTTCCCGAGGGAGCTGAAGGAGGTGTTTGCATCTTGGCGGCTGCGCTGCGCAGAGCGGGGCCGAGAGGACATTGCTGACAGGCTGATCAGCGCCTCGCTCTTCCTGCGCTTCCTCTGCCCGGCCATTATGTCGCCCAGTCTATTTGGGCTTATGCAGGAGTACCCAGATGAGCAGACCTCACGAACCCTCACCCTCATCGCCAAGGTCATCCAGAACCTGGCCAACTTTTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067629:ENSMUST00000194598:10
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:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGAGTTCATTCGTGCTCTGT
R:
GATGAGGGTGAGGGTTCGTGA
Band lengths:
347-1734
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