MmuINT0067617 @ mm10
Intron Retention
Gene
ENSMUSG00000038860 | Garnl3
Description
GTPase activating RANGAP domain-like 3 [Source:MGI Symbol;Acc:MGI:2139309]
Coordinates
chr2:33052096-33054257:-
Coord C1 exon
chr2:33054158-33054257
Coord A exon
chr2:33052215-33054157
Coord C2 exon
chr2:33052096-33052214
Length
1943 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATT
5' ss Score
8.83
3' ss Seq
ACTGACCGTCTCTTCTCTAGTCC
3' ss Score
8.49
Exon sequences
Seq C1 exon
AGTGCAGCTGCTCTGCCAGGCACTTGGCGAAGGACAGACGTGCACTTAGAAAACCCGGAGTACCACACCCGGTGGTATTTCAAGTACTTTTTAGGACAAG
Seq A exon
GTAATTATGTCCTTGTGGTGACTGGGGGAAGAGATTCTGTTCAAACCTGCATAATAATTTCAAGCACTGTGTATGAGTGGAATGCAATCATTCAGGACGACATCATCAGAGCACTTCACAGTGAGGTCAGGGGTGGGCTTCGTGGGCTAAAAGCTTCAACTCAGAGCGTTCTTGATTGTGGGTTGGTCTGTTGTGAGGAGTGCTGTGGGGGTTGGGGTTTAATGTTGTTTTAATCCCTGGTTAAGAGGGAACTAGCTCATAGGAATGAGTCCTTTGATAGATAAGAATTTTCAGGATGGAAAAAAGGCTTTAACTTAGCAAGGTCAGTACCTATCTGCATGAGTTCTAAACATTTCACTTGAGACCATGAAGGAGAACAATTGTTTCCTGAGCAACCTCTTGGCCATAAAACTGTGGGCTCTGCCATATTTACTCACCAATGACAAGTATTTGTCTTGTGGAAGTATATGTAGCTATGAGGTGCCGTGTGAAGTGAACCAAACCCCCTGCCCTCAAAAAGCCTATAGACAAGGTTTGCAACTTGGTTCTGCTCTTATTAGCCTTGGGACTTGAACTTGGCTTCTCTGTCTGTAAAGTGGAGCTGTTTTTAGTCCTTCCCTATAGGTCTAAACAAAGCTTCCAATGAGAGATGCAAGAATAACAATACTTGGTGCCTAACACATACCAAGAGCTCGGTTGCTCAGGTTTTAGACTATACATTTAGAGAGAGAGCGCATGGAAAGATGGAGAGCAGATGTGTTGCTAATGAGAGAAGGGCTGGGAATGGAGGGCAAGTAACTGATGTGAAATCTGAAATGGCAGAGATGTGCCATGGGGCATCCATTGTGGAACTTGATGCTCAAGCCAGGAAATGAGAGTGATGTCTTAAAAACCAGTTACAGGGCTCAGGCAGCAAGAGCGATTGCACTGCAACATGACAGCCTGAGTTCAAATCCCCAGCCCCATGTAAAAAATCTGGGCATGACTGAGCATGTCTGCAGTACAACACCGGAAAGACAAACAGGTAGATACTGGGAGCTCACTGGCCAGATAACCTGGCCAAAATGGAGAATATCCAATTAATAGAGAGATCCTATCACAAGGCAATAAAGCTGAGAGCAGTGAAGAAGATACCCAGTAGCCTCCCTTGACTTCCTAAGTGCACAGACAGGCATACACACCCACACATCCATGTTTGTGCAACACACACACACATACACACACACTCATGTGCTCCACATGAAAGACAAGGAAAACTGTTACAGTATTATTCTAAAAAGCTCTGGTCTGGCCAGGCCGGGTTACTTGGGTGGGTGGGGGATATAGAAGCATTTACCAAGAAAGCAATGTGCCGGTCATCTTCCCCATGGCTGGGCACCGAGTGCCCTCAGCACTGGCCTCACAGCAAAAGAGTTGCTGTGAGTTTGAATGCCACCAGCATCCAAAGAGCTGATGCAAAGCCTCAAACTGGATTAAACAAGAAGGAATCAAACAATAAAGTTTGAGGCCAACATGATCTACATAGCAAGCTACAGATCAGCCAGGGAAGGCTCTATGGTTGGTGGCAGCAAACAGTTCAGTGGTATCAGAGGACTAGAACCTTTCCCCTTTTTCTGATTCTCAACCTTAGTGTGATGGCTTTGCCCTCCTTAGGACCATACAATGGCTGCAGCAGCTTCAGACATCACCTGACACTACAACATCCAGAGGAGAGGGTCATCTTTAGAATGGGGAGCCTTTCCATAAGGCTCTTGGCAGATTTCTCGTCCGTCTCAGCCAGCATTGAATCACAAGTTCATTTCTGAGCCATTCGCTGGCCAGAGGGAAGTGGGTGCACGATAAGTGGTCAGTCCTACCCAAGTCAGCCTTGGGATAGCATGTGAGGGCTGGCCACTTCTGTTTGAAGGAACCAGCTGCATCCTTACTGACCGTCTCTTCTCTAG
Seq C2 exon
TCCATCAGAATTACATTGGAAATGATGCAGAGAAGAGCCCCTTCTTCTTGTCTGTCACCCTTTCTGACCAGAATAATCAGCGTGTCCCTCAGTATCGTGCAATTCTTTGGCGGAAAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038860:ENSMUST00000102810:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.135 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CAGCTGCTCTGCCAGGCA
R:
TGTTTTCCGCCAAAGAATTGCA
Band lengths:
215-2158
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