MmuINT0067588 @ mm9
Intron Retention
Gene
ENSMUSG00000026867 | Gapvd1
Description
GTPase activating protein and VPS9 domains 1 [Source:MGI Symbol;Acc:MGI:1913941]
Coordinates
chr2:34570725-34572902:-
Coord C1 exon
chr2:34572836-34572902
Coord A exon
chr2:34570851-34572835
Coord C2 exon
chr2:34570725-34570850
Length
1985 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAC
5' ss Score
5.88
3' ss Seq
CAGGATAAACATTTCTCCAGGTC
3' ss Score
4.46
Exon sequences
Seq C1 exon
GTTCTAAACATGCAGCTTTCGGATGGAGGACAAGGAGATGTCCCTGTTGATGAAAACAAACTCCACG
Seq A exon
GTAAACCTGATAAAACCTTGCGCTTTTCCCTCTGCAGTGATAATCTGGAAGGCATATCTGAAGGTGAAGGGTTACTTCATTCAGGGAGTGTGTGATTGAAGTTGTTCTGTGTTCTTTAAAGGAGCCTTATAAATTATAGTTAAGCCACCCATGCCTCTCACTAAGGAGAATAATGAAATTTCCTCTAATGAGCTTTAACATGACTATAAGATTGTTTCCTGAATAAAATTAAGATTGCAAGTGGCTGTTGGTCCTATAAAATGACCAAACATGTCAATGTTAAATGAGTAACAGCAAGTGTGGTTCTCAGTCTTGGTGTCGGCACAAGCTTATAGCGCTCCTTTAGAGGGATATAGTGCATGTGTAACTGCGGAGAGTGGATGCTGGCATTGCAGGATGCTGTGTACACGTCTTTACTGTTCTGTGTTCCTTTATCCACACACTCACACATGCCTTTATGAATCAGGTCACTGTGGAATAAAAAAGTCAGGTGAGGGTGTAGTTGGTAGAGTGTTTGCCTGGCATCCCTAGACTTAATCTTCAGTAGTGGTGGGGGGAAAAAAAAAGGAAACTCTTAAACCAGATTGTGAAGTTAAGAGTTTGTCATTCCATATGTTAGGGCAGTTCATTTTATGAAAAAAGTTCAAGTTTACTAACATTTAAAAGGAGACATAAATATCCTCTTTAACCTTTCAGAAAATCGCTGATATGTTCAATCTAGAAAATGTGGAAAAGAAATAAGCTTACCTGTAATTTCACTGTTCTCTTAAAAGTTAATGTTTGATTATTTAGAGCAAAATCAAGTTTATGATGTTTGTAACCCTTTTATGTTTCATTAACATTCCCTTTGTATTTTGTGTTTTTAAATAACATGCTTTTTTTTCCTTTCATTATTTTGAGACAAGGTGTTATTATTGTCCCTGGCTGACCTGGAATTCACTAAGTAGACCAGACTGAACTTGCCCTTAACAGAGTTTCTCCTACCTCTGGTTCCCAAGTGCTAGGATTAAAGATGTGGTCACCATGCCTGGCAATTCATCACCTGGGCAACAGGCAGGTTCATCTCTGGGTTGGAGGCCAGCTTGTCTACAGAGTGAGTTCCAGGCAGCCAAGGTTACACAGAGAAGCACTGTCTTGAAAAAAACAAAACCAACAAGCAAAAGAATTGTTTGGTTTGCTTGTCCTACCAATGGCTCGCAGATGGCATAGCTTTTAAACTGGCCATTAAACCTTAACCTTGACTGCGTTCATCTGGTTGGACATATGGCCCTTGGCCCTAATGATTCGGTCATTTGCAGAACATTTCCAAGGAACGTCCAGGTCCATGAACCTGCTGGCATTGTTCTGCATGTCCAGGCACTTCCTGCTTACTCTTTACTGCACACTAGCACAGAAAGTACTTCTTTTTTTTTTTTTTTTTTAAAGATTTATTTATTTATTTATTATATGTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGCATCAGATCTTGTTATGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCCGGACCTTTGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCAAAAGTACTTCTTTTTTAAGTATTATAGTAGCTCTTCAACAAGCAACCTTAGGTTATTTTTCTTATTAGTTTTTTAAAGATAAATTTCTAGAGGCAGACCTGTTGGCTCAAAGGCATTTATATTTTTAAGGAAATAAATAAAATATTAAAAGCATCTTAAATCAGGTATGATGGCACATATCTGTAATCGCAGGGTTCACAATGCTAAGGTAGAAGACTTGAAGAGTGTAAGATTAGTCTGGGCTATATAGTAAGGCCTTGTTTCAAAACAGAACAGAACAAAACCAGAAGAGAAATAAATACTATTTTCATGGCATGAAATATTACATAGTGACTTATGAATTTTTTAAGAAGATTGCTGACAGGATAAACATTTCTCCAG
Seq C2 exon
GTCCTTCCAATCGCTCCAATTCGGTGTCTTCTCTCGACCTGGAGGGAGAGTCTGTATCTGAACTTGGGGCAGGACCTTCTGGGAGTAACGGAGTTGAAGCACTGCAGCTGTTAGAGCACGAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026867-Gapvd1:NM_025709:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.998 A=NA C2=0.997
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF153241=TALPID3=FE(19.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTAAACATGCAGCTTTCGGA
R:
GCTCTAACAGCTGCAGTGCTT
Band lengths:
182-2167
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: