MmuINT0003724 @ mm9
Intron Retention
Gene
ENSMUSG00000026940 | 4921530D09Rik
Description
RIKEN cDNA 4921530D09 gene [Source:MGI Symbol;Acc:MGI:1924308]
Coordinates
chr2:25469078-25471033:-
Coord C1 exon
chr2:25470929-25471033
Coord A exon
chr2:25469201-25470928
Coord C2 exon
chr2:25469078-25469200
Length
1728 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATC
5' ss Score
7.46
3' ss Seq
GCCTTTGCCTGTCCTCATAGGTG
3' ss Score
10.99
Exon sequences
Seq C1 exon
ATTATCCGCCAACTGGAGAACAACATTGAAAAGACGGTGATCAAGATCACCACCAGCCAGAACATCCACACGCTGTACAAAGTGCTGCTGGATTACCTGAAGAAG
Seq A exon
GTAATCAGCCCCTTGGCCGGAGCCCCGCCTGCGACTCTCCTCCAGGCAGCCCGAGAGGTTGTCCTAAAGTATGTGGAAATGTACCTCTGAGAACTTCATTTTTGTTGTTCCACACAAGCATAGTATGGGCTGCACCCAGAATTTGGGCTTAAGCCTGGGCATGGTAGCACAGATATATGTATGATCTTAGCACTCAAGAGGCTAAGATGGGAAGATCCCAGGCCAGCCTGGGCTACACAGTGAAACTCTATTTCAAAAAGAGATGTGAATGATCACACACATCACAAAGTCACAGAATTCTTTCTTTTACATATGATATGGCTTAGTTTGGAACGCTGAGGGTCCAAGATGGGCCATGCCCACCCCCCATCCCCCAGGAAATCCTGTAACATGCTTCAGGAAAGACTCTTCTCCCTCTTCCCATAATATGCTGAGCACACAATCTCCTGCCCACTTTGGATCTGGCTCTCCCCTGCTTTCTACGAATCCAGGAGGAAGGAGAGACTGACCCACGGAAGTCCCAGGGAGCCACGGTCATTACTCTCACTGAGCGCACTCCCAATATGGCGCTCATAGAGCAAGAGCATCTGTAGTGGAGAAAGTGCTTCAGGGCAGCAGGGGCACCTAAGAGCACAATGGTGGACAGACCTGAAAAGGTGGCCAGGCAAAAATTAATACCCTCACCCTCACGCGAGATAGGGAGGTGAATGAGCGGCTTGGCTTGGGAGGAAGGGCCCGTGTGTGAGCAGTTACAGCAGCTTTTCCCTGCTGAGGTCACACGCCTGAGCCAGAATCTCAGTATCATGCTCTGGTCTGTCCCTCTGACCCGACCCTCATGCTGGAAGCTCAACTGGAAGCCCCCCTGTCTTTCCTATGTTCACCCCTTCCCACACCCCTTCACTGGGGTATCCTTTGTAGAACTTTCTTTCCATAACAAACACACTTGAAACAAATCCCCATGTTCAACCATACTTTTTTTTTAAATTGGCAAAGATTCAGCATGTATAGGTTTTGAAAGTAAAGTATTATCAATCCCCAGGCTGCCTTGACCATTGATGCAAGTGTGCTACCTTACAGCTCTATTCAGCCTAACAACAACCTTTGACAAAGTCAGCAACACCATTAAAGGGCTAGGTATGACCACAAGATCACAGAGCTGGCTGGTTAGAGGCGGCCTTCACTTGGAGCCCTATCTAGTTCTATGCCCACCTTTCTCTCTCTCTTTCTTAAAGATTTATTTGTTCCACTGGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACACAGGACCTCTGGAAGAGCAAGCAGCCAGCGCTCTTAACCACTGAGCCATCTCTCCAGCCCCCATACCCATCTTTCAAGCCCCTCTTTTCCACTTCAGATCAAAGATGTCCCCCAAGCAAACCCTCCTGGACTTTAGAGTTGGCCTTCGATGGGGTGGGTCTTTGAGTCATTATATCCTCTTGTCCTGGATAGTGAGAGTCATAGGTCACCAATGCCTACCCATGCTAGAACACTTCTTTCTCGTGCTCTGTACCTTGCCCAGATGCTGGGCCACAGTTGTAACCCCTATCGTGTCCTAGGGCTCACATAGTCTGAGCATGAAGGGTGGAAGAGAACCAAAAGGCCCAGGAAAGCCAGCAGTATGGGATGATGGCAGGAAAGGAATCCACGGCTTCATGACCATTTTTGCCTTTGCCTGTCCTCATAG
Seq C2 exon
GTGCTGGCAGAGTACCCCACAGAGCTAGACAAGCTCCAGAACCTGGTGGCCAACTACTGCTCGGAGCTGTCAGACATGACAGTCATGTCCCAAGATGCCATGATGATTACTGATGAGGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026940-4921530D09Rik:NM_029859:5
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=0.073
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
ATCCGCCAACTGGAGAACAAC
R:
GACCTCATCAGTAATCATCATGGCA
Band lengths:
222-1950
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: