MmuINT0019427 @ mm10
Intron Retention
Gene
ENSMUSG00000000325 | Arvcf
Description
armadillo repeat gene deleted in velo-cardio-facial syndrome [Source:MGI Symbol;Acc:MGI:109620]
Coordinates
chr16:18397297-18399145:+
Coord C1 exon
chr16:18397297-18398326
Coord A exon
chr16:18398327-18398961
Coord C2 exon
chr16:18398962-18399145
Length
635 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TGACTAGAGGCACATTACAGGCA
3' ss Score
-4.97
Exon sequences
Seq C1 exon
GTCACTAAGACGGTCAAGACTGTGACCACAAGGACAGTACGCCAGGTGCCTTTGGGCCCAGATGGACTCCCCTTGCTGGACGGCGGCCCTCCACTTGGCTCTTTTGCTGACGGGCCCCTGGACCGGCATTACCTACTTCGTGGTGGTGGTGGTCCAGCAGCCACACTCTCCCGAACCTACCACAGCAGTGGAGGTGGCTTTCCCGATGGCCCCGAGTCCCGTGATATTCCAAGCTATGGCAGCTTGTCCCGAGGGCTCGGGGTACGGCCACCACGTACTGGCCTCCTGGGCCCAGGACCTGGTGATGGCTGTTTCACACTGCCTGGCCGCCGAGAAGCCTTCCCCATGGGCTCTGAATCCGGACCACCAAGCGGCCGCTCTCTGCCTGAGCATTTCCAAGCTGAACCATATGGCCTGGAGGATGATACACGGAGCCTGGCTGCGGATGATGAGGGTGGCCCCGACCTGGAGCCTGACTATAGCACGGCAACCCGGAGAAGACCTGAGTACGGGCGGGGCCTTCGTGCCAGGGCCTTTGAAGACACAGCAGATGATGCTGGTGAGCTGATAGAAGAGCGTCCCCCATTTCCAGCAGCAACAGCCCCTCTGGCCCAGCCTGAGAGGGGCAGCCTGGGCAGCTTGGACCGAGTAGTGCGGCGCTCACCTTCAGTGGATAGCACCCGCAAGGAGCCACGCTGGCGGGACCCCGAGCTGCCAGAGGTGTTGGCCATGCTGCGGCACCCTGTGGACCCTGTGAAAGCCAATGCTGCAGCCTACCTGCAGCACCTCTGCTTTGAGAACGAGGGTATTAAGCGGCGAGTGCGGCAGCTGCGTGGGCTCCCCCTGCTTGTGGCATTACTAGATCACCCTCGGGCTGAGGTGCGGCGCCGGGCCTGTGGGGCACTGCGCAACCTCTCCTATGGCCGGGATACTGACAACAAGGCCGCCATCCGGGACTGCGGGGGCGTGCCAGCCCTGGTGCGCCTACTGCGGGCGGCCCGTGACAATGAGGTCCGTGAGCTGGTCACTG
Seq A exon
GTGAGTGGGCATTGGCCATAGCTGACATGAGCGTGGCTCAGCCCGAAATTGGGGAAACAGGAGTATAGCAGGCCCATGTTGTGGGATGGGTCCCCAACTCTCTCAACCATGGGGTTGCTGGCACCAGACCCTGTCGCCCTGGTTCCTAAACTGGAGCTTGTGCCTTGGAGAGCTTGGGAGTCACAGGACCGTGTCCATGGTCCTGTAGTCTCAGGAGCATTTGCCAGTCCACCCACTTGGGTGTAACAGGGAATGGATGGGATAAACTATCACTGGTTATGCCTCTTCTATAGTTTTTCCTTGTTAGCTGAAAGCTCCTACTAAGTGCTGCCTATACATACATCTTGTTGTACAGGGCCCAGAACCTCTTACAGCTTTCAGTGGTCCTTATGTGAACTGAGTGTCACTCAGTGTAAATGTTTGCCTAACATGTGCAAAGGCCCTGGGTGCCATCTTTGAGACAACTTCCTATCCCTGCTCTCCACCCCCACACCCCACAAAAACAGTAGCAACTATGCTGGGTTCAGGTGCTGGCTAGAGGACAAGGAGGGAAAGCAGAAGCAGATTGTGTCATCCCTGGGGAGGCCGAGGCAGTAGGGTCATGGTCAACAGTGTTGACTAGAGGCACATTACAG
Seq C2 exon
GCACACTCTGGAACCTGTCATCCTACGAGCCCCTGAAGATGGTCATCATTGACCACGGCTTACAGACTCTGACCCATGAGGTCATCGTGCCCCATTCCGGCTGGGAGCGAGAGCCTAACGAAGACTCGAAGCCCCGGGATGCCGAGTGGACAACAGTCTTCAAGAACACATCAGGCTGCCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000325:ENSMUST00000115613:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.706 A=NA C2=0.306
Domain overlap (PFAM):
C1:
PF0051418=Arm=WD(100=11.9),PF0051418=Arm=PU(81.0=9.9)
A:
NA
C2:
PF0051418=Arm=PD(16.7=11.3)
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:
GAGGGTATTAAGCGGCGAGTG
R:
AGTCTTCGTTAGGCTCTCGCT
Band lengths:
355-990
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