MmuINT1024226 @ mm10
Intron Retention
Gene
ENSMUSG00000039103 | Nexn
Description
nexilin [Source:MGI Symbol;Acc:MGI:1916060]
Coordinates
chr3:152236982-152238022:-
Coord C1 exon
chr3:152237665-152238022
Coord A exon
chr3:152237580-152237664
Coord C2 exon
chr3:152236982-152237579
Length
85 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGA
5' ss Score
6.91
3' ss Seq
TTCTCCTTCTTCTTTTCTAGTGG
3' ss Score
10.74
Exon sequences
Seq C1 exon
AAAAGAGAAGATGAGGAGGAAGAAGAAGGTAGCATTGTTAATGGCTCCACTACTGAAGATGAAGAGCAAACCAGATCAGGAGCTCCATGGTTCAAAAAGCCTTTAAGAAATACCTCAGTTGTAGACAGTGAGCCAGTCAGATTTACTGTTAAAGTAACAGGAGAACCCAAGCCGGAAATTACATGGTGGTTTGAAGGAGAAATACTGCAGGATGGAGAAGACTATCAGTACATCGAAAGAGGTGAAACTTACTGCCTGTATTTACCGGAAACCTTCCCAGAAGATGGAGGAGAGTACATGTGTAAGGCAGTCAACAATAAAGGCTCAGCAGCGAGCACCTGCATTCTTACCATTGAAA
Seq A exon
GTAAGAACTAATTGGCTTTTTGATCCTTTGTTTTATTAGGAAATAAATAGGAAAAAAAATCATCCTTCTCCTTCTTCTTTTCTAG
Seq C2 exon
TGGATGACTACTAGGCTTCCCTCTGTCCTTGGGACTCTCTCTCTCGCTGCATCTCTGTGGAGGGGCCAAAAAGGAGACCAGAGGTGCCACTATAACTGACTTAATCTTTCCCCAAATCTTCCTCTTAAGAACTTCTCATGCATATCAGGTTCATTACCATGCTGTGCAAAGTCAAAGCATAGCTGACAGAAAAGGGAAATAAATGTACCCATTCTGTCAGAACTAAGACAGAAGCTTCGTATTTATAGAACTAAGACTTAACATATACAGTTTGCATGAATAAACTGGAGATTTTTTTGCCATTGTCAATGAAAATGGACCGATCAGTAGATTTAGTAAAAAGTGATTTTCTAGCTTTAAAAATAAGTCTGTAAATGTCAAGTGTAGTGTTGCATGCCTTAATCTAAACACATGGGGGTAGGTGGATTTCTGAGTTCCACGACGGCCAGAACTATACATAGTGAGACCATGTAACCCTGGATCCTAACAACACAGTCTGTAAATAAAAGTTTATTATGTTCTAATATTGGGTGGTTTTATATTTAATTTTCTGGGAAACGTGTTGTGAAATCAAAATAAATTTACCTGTGCATTAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039103:ENSMUST00000046045:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.380 A=NA C2=0.320
Domain overlap (PFAM):
C1:
PF0767911=I-set=WD(100=75.0)
A:
NA
C2:
PF0767911=I-set=WD(100=73.2)
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGCCTGTATTTACCGGAAACC
R:
CTTTTTGGCCCCTCCACAGAG
Band lengths:
181-266
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