MmuINT0005279 @ mm10
Intron Retention
Gene
ENSMUSG00000006204 | 5430419D17Rik
Description
RIKEN cDNA 5430419D17 gene [Source:MGI Symbol;Acc:MGI:1918645]
Coordinates
chr7:131224962-131226767:+
Coord C1 exon
chr7:131224962-131225000
Coord A exon
chr7:131225001-131226619
Coord C2 exon
chr7:131226620-131226767
Length
1619 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TCAAATCCTCTTTCTTATAGAAA
3' ss Score
7.63
Exon sequences
Seq C1 exon
ATCCCCCATTGGCTGCCATGGAAGGAGCAACGAATCCAG
Seq A exon
GTGAGATCTCAGTGCTTGGATGTCTTCTTCCTTAGTGTTCAAGCCTTGAAGGAATTCTTCCAGGAAACTGTACCAGAATACCACTTATCTAGGTCACCCCACTAGAATTGTTCTACATGAAGAATCCCAAAGAAAAGGCCAGTGTACTTAGGGATGTGATTTCATGTCCAATCAGTCAAAGAAGGAGTTTCAAACAGAGACACAATGCCACTTCTGCATTCTCAAAGCCAGAGCATTGAGTGAAGGCTAGACACGGTCATTCATGTAATGATATTGCCAGTCAGAACCTAGAGCCATTACTTCAGAAGGGGTCCACTCTGAAGAGCATGCTTGCCTTCTCTGCCCTTGTCCTCTCCCCACACCCCCTTTCTCCACACTCTCTTCTTCATTTTCTCTTTTTTCTAGCTTTGACTATGTTTCTGGGTTCTAGAACTTCCAGTTGGCATAGCATAGACTTAGCACCATTTGATGACAAAAATCTAAATGATGATGATGATGCCAGAAGTACCTGGCTGGTCAGAACAAGTCTGCACACAGCCAGATGATCTGACTAGATACGAGTTCTTTACCCTGCCATTGAACTAAATGTTGGAGTAGACATATAGACAACCAGGTTAAAAAACAAAAACCAGACAGGCAAATGTGTGGACTGGTGGATGTAAAATGCTATCATTAATAGAAAGGCATATGACACAGGCCAGCTTCTTTCTACATAATAGCAGATATTTAATAACATCACTTTAAAAATGATGGTTGGGTGGGCCAGCTATTGTCATCATCACATACATACATAGAAGTCCCACACAGGTTCACTCTTAACTGAGAACACTGAAGCAGTGCATCACTCATTGGTTGTTTGAGATCATGAGATATTCATGGGCAGGATGTGATTGACAATGAATGACAGAATCCACAACTAAGGAATAATGAGAAAGTTCTTACCAATATTCATCTTCCTAGAAATCTCCATAAAGATGAGAGCTATATCAAACTTCAGACACGTGCATGCTAATAGCTTACGTTTACAAGATATTTTAAACCATTTTATAACTTCAATACACCCCAAGGCACATCCACAAAGTAATGACCAGTAAAACCTCTTTTTGAAAAAAGTGAAAAGAAAAAAAAGGTGTAAATTATAAAATCAGTAAACTGAACAATACACACTAAAGCTTTAAAGCACCTTTTCTTAGAATTTTATACAATGAGTATAGTGTAGTTGTACCATATCCACCCTCCTCCACCCTTCTAAATGCTTCTATGATCCCCCAATCCACATCTCAAATTTAGGCAATGTCTTTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCATCCATCCATCCACTTATCCATTCATATAGCTACCTATGTGAGTCCAGTTAGTGTTTCCCATGCGCTCAAGGGTTTTAGGACTGATCACTGGAGGAAGGACAACCTATCAGGAGCCTCATCCCTAGATAAAATTGACTGTCCCCCAGGAGCCATCTTCAGCTAGAGATGGGGAATCTCCTGTGAACTCTTCCTCCATCCACATTGGCATGTTGACTGATGTGCTTGTGCAATTTTGTTGTCAAATCCTCTTTCTTATAG
Seq C2 exon
AAAAATCTCGGTGTGGTGGAGTTATTACCAGTGCACCCGGAAAAATTAAGAATCCCCCAATGAATGAAATGCATGACAACATAACCTGTGTGTGGGAGATCAGGGCAAGCACCTCTGAGCATATACGGCTGGCGTTCCCATCTCTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000006204:ENSMUST00000050586:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.357 A=NA C2=0.100
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0043115=CUB=PU(43.3=90.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCATTGGCTGCCATGGAAG
R:
CAAGAGATGGGAACGCCAGC
Band lengths:
182-1801
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