MmuINT0038665 @ mm10
Intron Retention
Gene
ENSMUSG00000013465 | Nelfb
Description
negative elongation factor complex member B [Source:MGI Symbol;Acc:MGI:1931035]
Coordinates
chr2:25203141-25203490:-
Coord C1 exon
chr2:25203348-25203490
Coord A exon
chr2:25203248-25203347
Coord C2 exon
chr2:25203141-25203247
Length
100 bp
Sequences
Splice sites
5' ss Seq
CAAGTAGGA
5' ss Score
4.46
3' ss Seq
CCATGGCTTCTTGTATGCAGGTT
3' ss Score
6.68
Exon sequences
Seq C1 exon
GAGGCAGAGCTCATCACCAAGTTCCTGCCGATGCTCATGTCCCTCGTGGTGGATGACTTCACTTTCAACGTAGATCAGAAGCTTCCAGCTGAGGAGAAAGCCTCAGTCACATACCCCAACACACTTCCTGAGAGTTTCACCAA
Seq A exon
GTAGGACTCCAGGGCAGGTTTGGGGGAGGCATGAGAGTGGCGCTGCCAGGGAAGGGGCTGCCGGGCGGGCTGACTGAAGACCATGGCTTCTTGTATGCAG
Seq C2 exon
GTTTCTGCAGGAGCAGCGCATGGCTTGTGAGGTGGGACTATACTACGTCCTACACATCACCAAGCAGAGAAACAAGAATGCTCTCCTGCGCCTGCTGCCTGGACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000013465:ENSMUST00000059849:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF062098=COBRA1=FE(15.3=100)
A:
NA
C2:
PF062098=COBRA1=FE(24.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGCAGAGCTCATCACCAAG
R:
CAAGTCCAGGCAGCAGGC
Band lengths:
250-350
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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