MmuINT0005290 @ mm9
Intron Retention
Gene
ENSMUSG00000006204 | 5430419D17Rik
Description
RIKEN cDNA 5430419D17 gene [Source:MGI Symbol;Acc:MGI:1918645]
Coordinates
chr7:138388168-138390321:+
Coord C1 exon
chr7:138388168-138388385
Coord A exon
chr7:138388386-138390003
Coord C2 exon
chr7:138390004-138390321
Length
1618 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
TGGAATCTTCCTCTGTTTAGAAG
3' ss Score
5.95
Exon sequences
Seq C1 exon
CCTGGAAGATATCCTTGGATGTCCCTATGACTCAATTGAGATCTTCGATGGCCCCAGAATTGCATCACTCTCCATGGGGAAGTTTTGTGCCCCATCAGCTGTGGTATTTTTCTCCTCCTCAGACATCTTGACAGTGGTGTTCCGCAGCGATTATATGACAACAAACACTGGCTTTTATGCTTTCTTCAATGCAATTCCACAAGATGGAAGAGAGTCAG
Seq A exon
GTAGGAAGCTTCAGGAGATAATAGAGAACAATTTCTAAATCGACACTCCTATCACAAAGCCTGGGTAGATTTTAACCCAAACACACACACACACACACACACACACACACACACACACACACACACCTTACCTGCTAGAGGTGGTAGTATCACAAGGAGGTAGATTTTCTCACCATGGGGGTCAGGTTACCAAGCAACAATAAAATAGTAACATGCATCCTGTACAAATACTGCAAAGGGTGGTTGTAAAAGGCCAGGCAGTTTCCATGGAAAACCAAGCTCAATGAATGGTCTTCAGGCCGCATTTGCTATCACAAGGTCTTTGGGAACTGTCCAGAGTTCTGAAACATGGAAGCCCAACACTCCTCAAGATTTCACACACACACACACACACACACACCTTTACCTGTTGACCCAACTCACTTGTAGCATGCCTTAAACCATAGATGCACCCTAACTTGAGGCTTGGGGGCTCCTGCTATCCTTGGCCTCATAGACACTCATTGCAGAGCTAAGGAGCACTGCCTGTCAGTGGTGAGATAGCTGATGCTTAGATTCCCCTGCAGGAACTCCAGTAATTCTTTCAGACTGTCAGAAAACCAGATAAGTAGTAAGTTCCTGTCTGAGGTTTGGGCTTGCTTGTCTCTGAGGAAAGAAACTCCTTTGTGGGTGTGATCTGTGTATCTTATATGTGTGCTCTCCCTGATTGATCCTGAGAGCCTCTACGATAAACACTTGATAGAAGCATGACTTTAGAAATGAGGAAACAGCTCAGAGAGGTGAAGTTATTGTCATGTAGGGGGCAGTAGAATGAGATTCAACCCCAGTTTCTGTCTTACTCTATAACCCTTGGGCTTTTATGGCTTTTATGGAATCAAGACAACCTCAAGGGTTTGATGACCTTGGCCATGGATGGTACAGCTGCTAGGACTCTCTCTCTTTTTTCTTTCTTTCCTTGTTTCTTTCTTTGCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCTTTTCTCTTTTTTATTTTGGGGATTATAATATAATCACAACATTTCTCCTTTCCCTTTCCTCCAACCAAATTCTTCCATATAACCACCCACCCCACTGTTCTCCCCCCAGTTCCCCCCTCACACACTCCCTTTCCCCAGTCATCCTCCCCTCTCCTCTGAGAGGGTGCAGGCTCCCCTGGGTATTCCCCGCTCTGACACATCAAGTCTCTGCCATGCTAGGTGCATCCTCTCCTACTGAGACCAGGCAAGGGAGCCCATTTAAGGGAATGGGATCCACAGACAAGCAACAGCTTTAGGGACAGCTCCCACACCAGTTGTTGGGGGATCCACATGAAGACCAAGCTGCACATCTGCTACATATGTCTAGGGGTCTTAGGTCCAGTCCATGGATGCTCTTTGGTTGATGGTTCAGTCTCTGAGAGCCTTCAAGGGGTCAGGTTAGTTGACTCTGTTGGTCCTTCTGTGAAGTTCCTATCCCCTTCGGGGTCCCCACTCCTTTCCCCAACTCTTCTATAGGAGTCCTGGAACTCCATTCAATATCACTTTCTACATAAACTTCTCCATGTTCAAAACTGGAATCTTCCTCTGTTTAG
Seq C2 exon
AAGAAAGACCAGTGCTGCGGTTGGCAGGCAGCTCTGGACAGTGCTCGGGACGCGTGGAGATCCTCCACCAGGGGGCCTGGGGCACCGTGTGTGATGACCTGTGGGACCTGAATGAAGCTGAGGTTGTGTGCAGACAGCTGGGCTGTGGCCATGCCATTGCTGCTCCTGGAAGTGCCTACTTTGGTCCAGGCTCTGGAAACATCCTTTTGGACAACATTCAGTGTTCAGGAACGGAAAACCACTTTGGCCAGTGTTCCAGCTCTGCCTGGTTAGATCACAACTGTGGCCACCATGAGGATGCTGGCGTTATCTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000006204-5430419D17Rik:NM_175166:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(56.9=83.8)
A:
NA
C2:
PF0053013=SRCR=WD(100=91.6)
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
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGGCCCCAGAATTGCATCA
R:
AAGTAGGCACTTCCAGGAGCA
Band lengths:
353-1971
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: