MmuINT0005288 @ mm9
Intron Retention
Gene
ENSMUSG00000006204 | 5430419D17Rik
Description
RIKEN cDNA 5430419D17 gene [Source:MGI Symbol;Acc:MGI:1918645]
Coordinates
chr7:138386545-138388385:+
Coord C1 exon
chr7:138386545-138386698
Coord A exon
chr7:138386699-138388167
Coord C2 exon
chr7:138388168-138388385
Length
1469 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGA
5' ss Score
6.42
3' ss Seq
GCTTTCATCCCCACCCCCAGCCT
3' ss Score
5.66
Exon sequences
Seq C1 exon
GAGGAAGTAACTCTTGTGGAGGAGTCATTTCCAGCCTCTCGGGTTCATTTACGAGTCCACGGTACCCAGAAAACTATCCAACAGACATCCAATGTGTGTGGGAGATCCATGTGGAGAAAAATTTCCGCATAGAACTCATGATTCCGAATTTGAA
Seq A exon
GTAAGAAACTAGTTTTAAAGAGAGGGTTCGATCTGAATAAGAATATTGGGTTTCCTAGCTGTGGTAAGGACATTTTCTTTACTGATTGGAAAAAGCAGAGGAGCACAAAACATAGGAGCATTTCCAAATTCAAGTCTGAATTAATTTTGTAGCAGTACCTAATAGTTCTCTTCTAGCTAGAAAAATGCAGCAAGAATGTTTTGACATAGCTCAGCTTTGGAAATCTGTCTTTTATTTTTTTATTTTTTAATCTTATCTGATCTATTATTTTTATTAATTATTTTACTTATTTACATTCCAAATGTTGCCCACCCTTCTTGGTCCCCCTCCATGAGTTCTTCACCCCATCCCCCCTTCCCTTTGCTTCTGAGAGGGTGCTGTCCCACCCACCCACCCATCCACTTCTGCCTCACCCCACTAGCATCCTCCTTCCCTTAGGCACTAAGTTTTTACAGTGTTAAGTACATCTTTTCCCACTGACCCCTGACAAGTCAGTCCTCTGCTACACATGTAGTGGGGCCCATGGACCAGCCCACGAATGCTCTTTGGTTGGTAACTTAGTCTCTGGGAGCTCAGAGGGTCCCGGGTTAGTTGATACTGCTGTTCTTCCTATGGGTTTGCAATTCCCTTCAGCTCCTTCAGTCCCTCCCCTAATTCTTCTCCACCTATGTTCACATGAAGGTCAAAGGTCATTTCAGGTGTCATTTTTCAGGCACTATTCAACTTGTTTTTCAAGAGAGATTGCTCATTGGCCTTGAGCTCTTAAAGAAGCTAGGTCACCATAACCAGAATTTTCGCATGGGTTCTGGGGACTAAACTCAGGTCTACATGTTTAATGACAAGCACTTTACCCACTGAGCTATTGCTATAGATCCTGGGTTATATGCTTCTAGGCTTTGTCATGCTCCGGCATCACTATAGCTTACAAATGTCTTTACCATCCTCATTAAATATGAGGAAAATGAACAAATGGAGAGTAACTAGCTTGCCCGTTGACAACAGATGCAGGTCTATATGATGTCAAAGCAACAGTTCTTCACCAAAAGGTTTCTTCCAGCAAAATCTTTACAAGGCCTTTCTTCTCTGACATAGCACACACCATGCTGCAATAGAGCAAGATCATGAGATTCCATGATAAACCAGACTCAGCTAGGCCAAATCATGGTTCCATCAGCACTGTGCCAAGGTTGTTAATTTAGATTTGCTTTAAATCCAAGCAATCAGCGATCACAGACTCCTAACATATATTACCTTTGTGGCTGGTCAGAATCACTATAATTTTTAAAATTATGATAAAGTTGTATTAGTAAACTTCATATACTACCTAGGCAAAGAAAATAGAATCCTGATAAAGCATTTGAGAAAGTCTAATGAATACTACATGTTCTGAGATTGTCACATTTTGGGGCATTGATACTGAAGATGTTGCTACTGTGTCATTAACACCCAGCTTTCATCCCCACCCCCAG
Seq C2 exon
CCTGGAAGATATCCTTGGATGTCCCTATGACTCAATTGAGATCTTCGATGGCCCCAGAATTGCATCACTCTCCATGGGGAAGTTTTGTGCCCCATCAGCTGTGGTATTTTTCTCCTCCTCAGACATCTTGACAGTGGTGTTCCGCAGCGATTATATGACAACAAACACTGGCTTTTATGCTTTCTTCAATGCAATTCCACAAGATGGAAGAGAGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000006204-5430419D17Rik:NM_175166:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(42.2=88.5)
A:
NA
C2:
PF0043115=CUB=PD(56.9=83.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGAGGAGTCATTTCCAGCC
R:
CTTGTGGAATTGCATTGAAGAAAGC
Band lengths:
342-1811
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: