MmuINT1019705 @ mm10
Intron Retention
Gene
ENSMUSG00000073402 | Gm8909
Description
predicted gene 8909 [Source:MGI Symbol;Acc:MGI:3704134]
Coordinates
chr17:36164444-36165022:-
Coord C1 exon
chr17:36164977-36165022
Coord A exon
chr17:36164677-36164976
Coord C2 exon
chr17:36164444-36164676
Length
300 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
CCCTGTTCTCCTTTCCACAGCCA
3' ss Score
11.09
Exon sequences
Seq C1 exon
GCAGCAACAGTGTCCAGGGCTCTGCCTTGTTTCTGGAGGCCTTCAG
Seq A exon
GTAAAAAATAGGACCGGGGATTGGACCTAAGGCAAACAGAAGAGGACTGGGTCCCAGGCCCTCTCAGATTTACACCTTTGCATGAGTGGTGGGACTTGGAGATGGTTTCATATTGAATGTCCTGACTCTTATTTTTATACCCTGAGATAGCCTTCCTGTGGGAACAAGTTCTGACTTAGAAACTACAAATGTCTAAAGCTATTTGCTTTTCCTCTATGCACAATGGGAAGACCTGGAAAGCCCAGGATACCTTGGCACACAAGGACCCTGTCCCTAACTTCCCTGTTCTCCTTTCCACAG
Seq C2 exon
CCATCCTTCCTGATCCAGCAGGCACTAGGGGACATCTGCATCCTGTCAGCTCCATGCTGCCCTGAGCTGCAGCTCCTCACATCCACACTGAACATAAGAATCTGAATGTGAACTCAATTGAATCTGAATTTGAAATAGAAGAAAGTGGCTGGTTTCTGTCCTTGAGAAAATAATCTGTCTGAAATTAAATCAGAGCTTTAGATTAAGGGCCTTGGCAGAGGAGACTTCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073402:ENSMUST00000040467:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF066236=MHC_I_C=PD(50.0=81.2)
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCAACAGTGTCCAGGGC
R:
CTCCTGAAGTCTCCTCTGCCA
Band lengths:
278-578
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types