MmuINT0067583 @ mm9
Intron Retention
Gene
ENSMUSG00000026867 | Gapvd1
Description
GTPase activating protein and VPS9 domains 1 [Source:MGI Symbol;Acc:MGI:1913941]
Coordinates
chr2:34582736-34584694:-
Coord C1 exon
chr2:34583851-34584694
Coord A exon
chr2:34582823-34583850
Coord C2 exon
chr2:34582736-34582822
Length
1028 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
ATCATTGCTTTTGTTTGCAGGTT
3' ss Score
9.86
Exon sequences
Seq C1 exon
TGCTGAAGCTTCCCCTGCTGAGTGTTGCCAGCATGCCAAGATTTTGGAAGATACACAGTTTGTTGATGGATATAAGCAACTGGGATTTCAGGAAACAGCTTATGGAGAATTCCTGAGTCGGTTAAGAGAAAATCCACGACTTATTGCCTCCTCTTTGGTTGCTGGAGAAAAACTCAATCAGGAGAACACACAAAGTGTTATCTACACTGTTTTTACCTCCTTGTATGGCAACTGTATTATGCAAGAAGATGAAAGCTACCTCCTTCAGGTTTTACGATACTTGATTGAATTTGAACTTAAAGAAAGTGACAACCCCAGGCGCCTTTTGAGGAGAGGAACTTGTGCCTTCAGCATCTTATTTAAACTTTTTTCTGAAGGACTGTTTTCTGCCAAACTTTTCCTTACGGCTACTTTGCATGAGCCAATCATGCAGCTCCTCGTAGAGGATGAAGACCACCTGGAAACAGATCCAAACAAGCTGATAGAGAGATTCTCTCCAGCTCAGCAAGAAAAACTCTTTGGAGAGAAAGGCTCAGATAGATTTAGGCAAAAGGTTCAAGAAATGGTAGATTCCAATGAGGCTAAACTAGTGGCTTTGGTGAACAAATTTATTGGTTATCTTAAACAGAATACATACTGCTTTCCACATAGTTTGAGGTGGATTGTGTCACAGATGTACAAAACTCTTTCTTGTGTAGACAGATTGGAGGTTGGGGAAGTCAGAGCAATGTGTACCGATCTTCTGCTGGCTTGCTTCATTTGTCCTGCAGTTGTCAATCCAGAGCAGTATGGGATAATATCTGATGCTCCTATTAATGAGGTGGCAAGATTTAACCTGATGCAG
Seq A exon
GTATGGTTTTGCTATTATTATTATTTTAAGATTTACTATTATTTGCTATTATTATTATTTTAAGATTGCTTTAAATGCAATCAAACAAAAGTGATAAGCATTTAAAGCACAAACAACAATAACAATGACAACAAAACGTTGGTTGGAGGTGGAGAGATGGCTCTCTGGTTAAAAGTGTTTGTTACTATTGTAGAACTGAGTTCAGTTCCCAGTACCTACGTCAGATAGCCACTACTTGTAACTCCAGGGGATTCAACTTCTAGCTTCCATGTTCAGGTATACACACTTAAGGGAAAAAAAAAAATCATTGTTTCTTGTCTGCATGGTGGCTCACACCTTTAATCCCAACACTTGGGGCAGAGGCAGCAGATCCCTGTGAGTTGGAGGCCAGCATAGTCTATATAGCAAGTTCTAGGGCAGCCAGGGCTACACAGACCCTGTCTAAAAAAGCAACTGAAAACTATAAAGAGAATGCTTTTCCCTGTATTTGTGTTATACTTGAAGTCATTTATTGTGTGAGTTAGCCTTTGCAGATACTTAAAATTTTTTCTTGGGGCAGAGGTAGTTTGGGAATAAAAATGTTATGTAAGCTTGACAATTTGAATTTCATATCTGGGACCTATGATAAAGGAGAGAGCCAACTTCCAAAAATTGTCTTCTGACCTCCACATGTGCACCGTGACACGCATGCACACACATACAGTAATAATAAAGTGTAAAATATTTTTAAGCACACAAAGTACAATACCAGAAACAAATAAACTGTGCTTTCAGTTTCCTCGTGCTGCTGTCATGTGCTAAGAAGGAATTACAGCAACGCTTTCTACTTCCTCTAATTCTTAATCTGAAAATAACAAAAGCTGACAGAGACAAGATACACATTTTATTGGGAACATTATTTTGTTTGCTAGATCAGATGAATATGAATATTTTTGTGAAACCAGATTCTTAGACTGGAATGGAAGTGCTTTCAAAAACCAGTGCTGGTGTGTGCACCCACATCTGCTTATCATTGCTTTTGTTTGCAG
Seq C2 exon
GTTGGCCGCCTTTTGCAGCAGCTAGCAATGACTGGCACTGAAGAAGGAGATCCCCGGACCAAAAATAGCCTTGGAAAATTTGACAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026867-Gapvd1:NM_025709:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.239
Domain overlap (PFAM):
C1:
PF0061614=RasGAP=PU(94.6=67.7)
A:
NA
C2:
PF0061614=RasGAP=PD(4.5=31.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAATGAGGCTAAACTAGTGGCT
R:
AAGGCTATTTTTGGTCCGGGG
Band lengths:
344-1372
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: