MmuINT0005279 @ mm9
Intron Retention
Gene
ENSMUSG00000006204 | 5430419D17Rik
Description
RIKEN cDNA 5430419D17 gene [Source:MGI Symbol;Acc:MGI:1918645]
Coordinates
chr7:138368476-138370281:+
Coord C1 exon
chr7:138368476-138368514
Coord A exon
chr7:138368515-138370133
Coord C2 exon
chr7:138370134-138370281
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
ENSMUSG00000006204-5430419D17Rik:NM_175166:10
Average complexity
IR-S
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
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
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
Other AS DBs: