MmuINT1032591 @ mm10
Intron Retention
Gene
ENSMUSG00000067629 | Syngap1
Description
synaptic Ras GTPase activating protein 1 homolog (rat) [Source:MGI Symbol;Acc:MGI:3039785]
Coordinates
chr17:26964827-26966973:+
Coord C1 exon
chr17:26964827-26965038
Coord A exon
chr17:26965039-26966882
Coord C2 exon
chr17:26966883-26966973
Length
1844 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ACTGAAGCCCGTCCCTTCAGGCT
3' ss Score
4.16
Exon sequences
Seq C1 exon
GTGAAGGAGTATGAGGAGGAGATACATTCGCTGAAGGAGAGGCTACACATGTCCAACCGGAAGCTGGAAGAGTATGAGCGGAGGTTGCTGTCCCAGGAAGAACAGACCAGCAAGATCCTGATGCAGTACCAAGCCCGCCTGGAGCAGAGTGAGAAGCGCTTGAGACAGCAGCAGGTGGAGAAGGACTCCCAGATCAAGAGCATCATTGGCAG
Seq A exon
GTGAGGGGCGGCCCGGGGAGGGAGGAGGGGCTGAGGCTGCAGGGAGAGGGAGAGGGGGAAACCTGCTTAAGGCATTGAGCTGCTCTTACTGCGGCCCGCCACTGCTTGCACACTAACTCCTGAAGCCCTAGAGATACACCAGTGACTGTAGCCTAGCCACCAGTGTCTGGACTTAGGCCTGGACTCCCTATCAGTTCTTCTTAGCCCAGCCTGTGGGGTTCACCACAGAGCTAAGAGGCAGTTCCTAGCCACAGGAACTCTTAATCACTCCTGTGTCCCTGGCCAGAGCTCCTTGCCCAGGCTTAGAATGGGTTCCATTAGAGGGCTTTTAGCTTGTCAGTGTTCCAAAGAACCTGCCTCCTCAGGGGCTATCACAGCCAGCGCCAGCTGCACCCAGATCTGCTGTAATGTTTTGAGTGAGATTTAATTAGAAGAAAATGGTCTCTGCCTGAGACACTTGAAGTCCATGGCAAGGACTCTCTTATGAGATGAGTCCTCAGTAACTCGTGCATGGTGCACGGGGCCCAGAAGCTCCATCTCTGCACACAGGGTCTCTAGGAGGCCGGCTGAGCTGGGGGATCTGGCTGGCAGGAGACTTTGAGATACAGAAACCTAGTTGTACAGAGTTGTGCACACTTTTGTGGTTTTTTCCAGACAGGGTTTCTCTGTGTAGCCCTGGCTATCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCAAACTCAGAAAATTGCCTGCCTCTCCCTCCAGAGTGCTGGGATTAAAGGCGTGCACCCACACTACCTGTTTACTTGTGCACACTTTGAATCCAAGCTTTCAGGTGACAGAGGCAGGTGGATCTCTTAGAGTGTGAGGCCAGCCTGGGCTACATAGAGAGTTCTAGCCAGGGCTGCATAGAGAAACCTGTCTCAACAAACAAACAAACAAACAAACCAAACAGACAAACAATGACATAGAAATCTCACCAGGAGCACCCATGGCTGTAATCCCAACGTTTAGGAGGCGGAGGCAGGAGGATACAGCTACACAGGGCGTTCTAGGCTTCCCTGCCTAGAATGTGAGACACTATCTGAAAACCACAAATCAAGTCTACTTTCATGAGTTTGAGGGATGAACTCAAGTGCTTAAGAGGATATACAGCTCTTCTAGAGAATCTGAGTCAAATTCCCAGCACCCACTTCAGGTAGCTTATAATTGTCTGGAACTCTAGCTACAGGGGCATCTCATACATCTGGCCTCTGCAGGCTCCTGAACTCGTGTGCACAGACCCACACACAGATACACACAGTGAAAAATATATATAGGCTTGGCGGTGGTGGTGACACAAGCCTTTAACCCCAGCACTCTGGAGGCAGAGGCAGGCAGATCTCTGAGTTTGAGGCCAGCTTGGTCTAATAGAGTGAGTTCTAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTTGAAAAACAAAGCTGGATATGGTGACACATGCCTTTAATTCTATCACATGGGAGGCAAAAGCAGGCAGATCTCAGTCTAAGGTCAGCCTGTCTACACAGTGAGTTCCAGGCCAGCCAAAGATACACAGTGAAACTGTCCCCCCAAAAAACCAACCAACATACATACATAATTACATACATGTCTTTAAAAAGGCCCCAGAAGGTAGGCATGAAGATCCATGGGAGAAAGTGGAAAGCAAGACTCTGGTGACAGGCATCTTTTAGGTAATGGGGGAAGAAGAATTCTGCGAGGGGAAATATCAGAGGTTTTTCCAGATATGCAGGGGTTCCCCAGGGTCAAAAGTACCTCAGGTGGGCTCTGAGTCCGTGCCCGCCACTAACCCCACTGAAGCCCGTCCCTTCAG
Seq C2 exon
GCTGATGCTGGTGGAGGAGGAGCTGCGTCGGGACCACCCCGCCATGGCTGAGCCGCTGCCTGAGCCCAAGAAGAGGCTGCTCGACGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067629:ENSMUST00000194598:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.722 A=NA C2=0.654
Domain overlap (PFAM):
C1:
PF147121=Snapin_Pallidin=PD(56.9=46.5),PF120043=DUF3498=FE(68.6=100),PF071957=FliD_C=PD(67.2=63.4)
A:
NA
C2:
PF120043=DUF3498=FE(24.6=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:
GTGAAGGAGTATGAGGAGGAGA
R:
CGTCGAGCAGCCTCTTCTTG
Band lengths:
298-2142
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