MmuINT1032596 @ mm10
Intron Retention
Gene
ENSMUSG00000067629 | Syngap1
Description
synaptic Ras GTPase activating protein 1 homolog (rat) [Source:MGI Symbol;Acc:MGI:3039785]
Coordinates
chr17:26953030-26955081:+
Coord C1 exon
chr17:26953030-26953151
Coord A exon
chr17:26953152-26954927
Coord C2 exon
chr17:26954928-26955081
Length
1776 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGT
5' ss Score
9.39
3' ss Seq
TCTGACCCCTGTGCTGCCAGGGC
3' ss Score
6.95
Exon sequences
Seq C1 exon
CAAGGCTTCCTGAGCCGGAGGCTAAAAAGCTCTATCAAACGTACAAAGTCACAACCCAAACTTGACCGGACCAGCAGCTTTCGACAGATCCTGCCTCGCTTCCGAAGTGCTGACCATGACCG
Seq A exon
GTAGGTACTGGACCTGAAATTAGATGGGGACTGAGAGGAGTGGGGGATTCCCTGAGAACAAAGGTTAACGGGCTCATGTTGGTCGGGGTGCAAGAGACATCTGAGAGGAGCTGGCCTAAGCCACGAGTAACCAGAAAGAAGTGGTGACAAGGAAGGACCTGCTGAGGCAGGGAAGGAGGCGAAGGTGAAGCCAAGGAGGGCAGGACTCGTGGGGAGGAAGGAAGGTGGCTCCCACCCTGGGTAGGACTAGTGACAGAGCTTACTGGGTGGTGAGAAGAAGCCAATAGGACCCACCCAGGTGGGAGGTGAAGAAGGGCAGGGATTAGGGACAGCAGGCTGGACATGGGTAGCTGGTGTTGAATGAGAAGGATGAGGGCTCTGAGGTCCCAGTAGCAGGGCCAGTGGGGAGCAAGAGAACAATAGGAAAGGTAGCGTCTGGTATGCAGGTAACAGAATGGGGACAAAGGCTGGGGTTAATTCAGGGCCTGAGGAATAAGGAAGGAGACCTGGCTGCTTGCCTTTGTCCTTCTCTGGGCTTCCCCTAGTCCAGTCACTCCCTGGAGAGAGTCTGTCCTTTTCCCTTGTGTCTGGCTGTCCTAGGGACTGAGCAGGGTAGGAAGGTTGGGATCAGGTGAGTCACACCTTTCCCTGCCCCCTTCCAAGTAACCAGTGCTGGATTTGGGGCTGGAGGGGGGGGGGTGAGGGCATGGTATTCCTGGCCGCGGGGGCGGGGGGGGGGGGCGCCGGGGGAGCGTGGTGCTGACGGCAGCCAGAGCCTGTGATGACGGGGCTGCTATAAATAACTTCATGGAGGCTCCCACACCCGAGCTCCCCTCCTGCTTCCCCATGCTCTCCATCTTGGTCCCCTACCCATTTCCACACCACTTGCTATCTATCCTTTCTCCCCTTGCTCGGGTACCTCAGCCCGGCTTGTCCTGTGCTCCCCGCGCAGCACAGCGCAGCGCAGCGCTGTCCTCTGCACAGCACACGCTTGCTCTTCCTTAGCCTTACTGCGCCTGCTTTTGCCCCCTGCTTGCTGTTCTGCCTCCCCTTCTTCCCAAGTCTGCTTTCCAGCCTCTGACCTTTACTCTGCCCCGTCTGCTCCTTTATTTGCCTGGGCCTTTCTCTCTTTATCTCTTGGTTGTACTAAAAACTTACTTCATTTATAGTTTGAATCATAAAATGTTTATTAGGCACTAACTGTGTGCCAGGTCCAAACCAAACATTACTGTATTTCCTCTGTGACTCGAGTCTTTGCTTCCAATTTTTTCCTTTATATTGAGATTCTCATTTCTGGAGTCACCTAGACATGTCCAGGCCATTTTGTTTTTTCTTTCTTCTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTCCTTTTCTTTTGTTGTTGTTGTTGTTTCGTTTTCGACATGGTTTGTGTTTGTTTTTAAAGATAAGGTCTCACTGTGTGACCCTGGCTAGCCTGGGGCCTGCTATGTAGACCAGGCTGGCCTCAGACTTAACAGGGATCTACCTGTCTCTGCCTCTTGAGTGCTGGGATTAAAGGTGTGTGTTACTACGCCCAGCAGTTCTGAGCTATTTCTAGGTATCCTGAGTATGAGTTGATGCAGATAGGTCTCTTGAAGGGTTTTGGTTCCCCCCTGCGCCCCCCACCCCTACCCCGTACCTCCCACATCCACAGGAGGAGCCTGGGCTTCCTCTGGTGAGCAGAGTCCTCAGTGAGGAGAGAGGACCTTCCCTGATGTTTTTCTGACCCCTGTGCTGCCAG
Seq C2 exon
GGCCCGGCTGATGCAGAGCTTCAAGGAGTCACATTCCCACGAGTCCCTGCTGAGTCCCAGTAGTGCTGCTGAGGCCTTGGAGCTCAACCTGGATGAAGACTCCATTATCAAGCCAGTACACAGCTCCATCCTGGGTCAGGAGTTCTGCTTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067629:ENSMUST00000194598:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.383 A=NA C2=0.221
Domain overlap (PFAM):
C1:
PF0016924=PH=PU(24.8=65.9)
A:
NA
C2:
PF0016924=PH=FE(46.8=100)
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:
CCGGAGGCTAAAAAGCTCTATCA
R:
CTCAAAGCAGAACTCCTGACCC
Band lengths:
262-2038
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