MmuINT0003716 @ mm9
Intron Retention
Gene
ENSMUSG00000026940 | 4921530D09Rik
Description
RIKEN cDNA 4921530D09 gene [Source:MGI Symbol;Acc:MGI:1924308]
Coordinates
chr2:25472506-25473198:-
Coord C1 exon
chr2:25473055-25473198
Coord A exon
chr2:25472628-25473054
Coord C2 exon
chr2:25472506-25472627
Length
427 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
GTTCCCTCCACCACCTACAGAAC
3' ss Score
7.51
Exon sequences
Seq C1 exon
AATCTGAGCAGGCAACTGCACAGGAAGGGTGAGAGGCACACAGAACCCCTGGAAGGGGGGGCCGTTAGGCCACCATGAAGGTACACAATGAAGCAGCTGTGGAGGCACAGATAACGGAGCTAAGGACCATCACTCGGCTCCAGG
Seq A exon
GTGAGCCTCACACTGGGCACTGCCGCTCTGCTCCGCTACCAGGCAGCTGTCCCTCCTACTACCCACCCAGGCCCCAGCAGTGGGTCAGAGTCACAGAAGGGCCTGCCATCTGAGGGGTGACCTGTGCATTTCCCACAATATTGGCCCAAAGGTGGAGGGGTCAAGGAGAGGTCTGCCTGTTTCTCTGCAAGAGAAAGAGACAAGGGTGTCCCACTTCCTTGGTGGTCCTGGCCTCACCCTCTTTACTGGCCAGCAGATGACCACTTTGAGCAGGAAAGCTTGTGAAGGCCAGAGCAGGGTGAGAGGAGAGAAAATGATCACAAAAGCAATGCAGTATTCCACTGACCTCTCTGGATGCTTTGCGGAGATTCTCAGCCAGTCCTTTTACCCTACAGTCTGGAAATCTTGTTCCCTCCACCACCTACAG
Seq C2 exon
AACAATGTCGGGCACTCCAGATCCAGGGTGTGAAGGAGAAGACAGCACAGAACAAAGCTACAATGGGAATCCTGCGCAGCAACCTCCGCCGAGGAGCCCAAGACTGGGCTTTGGCTAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026940-4921530D09Rik:NM_029859:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.042 A=NA C2=0.098
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion 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:
CAACTGCACAGGAAGGGTGAG
R:
CTTCTTAGCCAAAGCCCAGTCT
Band lengths:
254-681
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: