MmuINT0067613 @ mm10
Intron Retention
Gene
ENSMUSG00000038860 | Garnl3
Description
GTPase activating RANGAP domain-like 3 [Source:MGI Symbol;Acc:MGI:2139309]
Coordinates
chr2:32990564-32992261:-
Coord C1 exon
chr2:32992123-32992261
Coord A exon
chr2:32990780-32992122
Coord C2 exon
chr2:32990564-32990779
Length
1343 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TTTTCCGAATTGTGTTTCAGGTG
3' ss Score
11.15
Exon sequences
Seq C1 exon
TCAGATATATACTTCACAGCAGCCACGACTGTGCATGAAGGCTCATCTGGAGGCAGCTCAAAGGGAGCCAGTGCCCACACGTCTCCTCAGACACCACCAGCCCGGGACACTCCACTGTTTCCTTCTTCCCTGGGGGAAG
Seq A exon
GTAAAGTCTAGCTTTTCCTGTCTTCTTAATACACGCTTTAGAGCCTGAGGTCTTAGGGTTATTGTCAGAGCTACACCTGCTATAAAAGTACTATTCAGGCCGGGCATAGCTCCATGCGCCTTTAATCCCAGCTCGCAGGAGGCAGAAGCAGGCAGATCTCTGAGTTCCAGGACAGTCTGGTTTACAGATCGAATACCAGGGCAGCCAGGACTACACAGAAAAGTCCCATCTTGGAAAAAAGAAAAAACAAAACAAAATTGTACAAGAAGTAGTTGTTGACATTGTCACTGTCTAAAAAGGAAGAACTTGTTTGGCTCTGCTCCCAACACTTGCGCGGTGAATGAAACAGAGAATCCCACACGTACTCAGACAACAAACAAAAACAGGCGAAATCCTGTTATGCAAAACATTGCTTCAGTGTTCCAGAGTGCATGCAGCTGCAAGCTTCATGTGTTTCTCCTGGGGGGTGGGCTAGTGGGTTTCATAGGGGAGATAGTGGGTTTCATGGGGGTGCTAGTGGGTTTTGAGGCTAAATCTTCAGCCCTCAGGCCACAGTGTGTCACTCTAGGTTTGCTGATATCTCAGAGGCCTTTGCCAAATTCCTGTGGGGCTGGGAACAGCAAGGGTTTTTGTAACTCCTTGCCCATCAGTCATCTTTATTGTTTATTGTTAGGATGAGTGTCCCAGGCGCAGGTCCTTGCTCTCCTTGCCTTGACTATTTTTCTGTGTAAGCACAACTGGCAGCAAGTGTATTTTATCAAATTCACTCAAGAAAAGGGAAGCTTTGCAGCAATCGGGAAAAAAGTGAATAAAAAAATAAATTAATAGAAAAAAAGGAAGGAAGCATCTTCATGCTAATTATGTGAAGAAACAAGGAGTTATTTTCAGGCCAGCAAGATGGTCCTGCAGGTAAAGGCACTTGCCATCTGGCCTGACGAGCTGAGTTGGATCCCTGTGTCACAGATGGAAAAAGAGAGCTGAGTCCTGGGACATCTGACCTCCATACATGGACACATGTGCACATACAATAAATGTAATTTAAACCTTTTGGGGAGTTTTGTTTGGTTTGTTGGTTTTGTTGTTGTTGTTTGTTTGTTTGTTGGATTTTTTTTTTTAAGACAGGGTTTCTCCATGTAGCCCTGGCTGTCCTGAAACTCTCTGTATAGACCAGGCTGGCCTCAAAGTCAGAGACCCACCTGCCTCTGCCTCTGCCTCCATAGTGCTGGGCTTAAAGGCAAACACCACCACTGCCCAGCTTGTACTTTAAAACTTTTAAAGAAAGAAGTTGTTCCGTTATAATTACATGAGCCTAAAGTTCTGGTCTTTTCCGAATTGTGTTTCAG
Seq C2 exon
GTGAAATTCAGTCTAAAAATCTGTACAAGATTCCACTTAGAAACCTTGTGGGCAGAAGCATCGAGCGACCTCTGAAATCACCCTTAGTCTCCAAGGTCATCACCCCGCCCACCTCCATCGGCCTTGGAGTCGCTGCCATTCCTGTCACGCATTCCTTGTCCCTCTCCCGCATGGAAATTAAAGAGATTGCAAGCAGGACCCGCAGGGAACTGCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038860:ENSMUST00000102810:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.596 A=NA C2=0.274
Domain overlap (PFAM):
C1:
PF0078017=CNH=PD(0.1=0.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATACTTCACAGCAGCCACGAC
R:
AGTTCCCTGCGGGTCCTG
Band lengths:
342-1685
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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