MmuINT0038659 @ mm10
Intron Retention
Gene
ENSMUSG00000013465 | Nelfb
Description
negative elongation factor complex member B [Source:MGI Symbol;Acc:MGI:1931035]
Coordinates
chr2:25209854-25210537:-
Coord C1 exon
chr2:25210438-25210537
Coord A exon
chr2:25210085-25210437
Coord C2 exon
chr2:25209854-25210084
Length
353 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CTGTGGTGTTTACTGTGTAGGTT
3' ss Score
8.19
Exon sequences
Seq C1 exon
GTACAAGAAGCTGGAAGACCTTCTGGAAAAGAGCTTTTCTTTGGTCAAGATGCCATCCCTACAACCAGTGGTGATGTGTGTTATGAAACACTTGCCCAAG
Seq A exon
GTGAGAACTGTGGGGCCAGCCTCTCAGACTGTGTGTTTAGTGCAGGAAGTTGCTTAGCTCTGGGAAAGTTTGATGGACTTGCCCTCCAGCAAGCTCTGGGCCCCTTCTTTATATCACACACTTCCCCTGGTTGAGCCAAATGGAAATATTTATCCCTTGAAGTGCAGGGTGGGTCTTTTGTGGGAAGAGGACTGTGGAGATTCTGGATGCCTGAATTCACCTGCTAAGAGTTGGAGGTCCATCACAGTCTGGGCTCTGTAGGGTCTGTGGGCAGCTGAGGCCTCATGGAGGCAGCTGTGTCCTCATGGCGACACAGGCAGGGCTTGCAGGGAGCTGTGGTGTTTACTGTGTAG
Seq C2 exon
GTTCCTGAGAAGAAGCTGAAGCTGGTGATGGCTGACAAGGAGTTGTACCGGGCATGTGCTGTGGAAGTGAAGAGGCAGATTTGGCAAGACAACCAGGCTCTCTTTGGTGATGAAGTCTCACCACTGCTGAAGCAGTATATCCTAGAGAAAGAGAGTGCGCTCTTCAGCACAGAGCTCTCTGTGCTGCACAACTTCTTCAGCCCTTCCCCCAAGACCCGGCGCCAAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000013465:ENSMUST00000059849:3
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=PU(84.2=47.1),PF062098=COBRA1=PU(0.6=2.9)
A:
NA
C2:
PF062098=COBRA1=FE(16.0=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:
ACAAGAAGCTGGAAGACCTTCTG
R:
GCCGGGTCTTGGGGGAAG
Band lengths:
318-671
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