MmuINT0151663 @ mm10
Intron Retention
Gene
ENSMUSG00000026532 | Spta1
Description
spectrin alpha, erythrocytic 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:174213862-174214253:+
Coord C1 exon
chr1:174213862-174213961
Coord A exon
chr1:174213962-174214055
Coord C2 exon
chr1:174214056-174214253
Length
94 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
CTCTCCTACTTTCCCCACAGGAG
3' ss Score
12.32
Exon sequences
Seq C1 exon
TGATCTAGAGAACTGGATCAAAACCATTGGCGGTGTGATATCATCACCTGAGCTGGCTGAGGACTTAACTGGCACAGAGATCTTGCTGGAGCGACACCAG
Seq A exon
GTACAGCTACAAACTCCACAGCCACTGGCCACTGATTTAAAACTCTCTCTTCTCACTATAGTATTCACTAGCCCCTCTCCTACTTTCCCCACAG
Seq C2 exon
GAGCATCACGATGACATAAAGAGAGAGGACCCTACCTTCCAGGCCTTAGAAGACTTTGGTACAGAACTTATAGACAGCGGCCACCGTAACAGACGTGAAATTGACAATACTCTCCAGAATATTAATTCAAAGAGAGACAATTTGGAAAAGAGTTGGGAAAACCGCAAGAAGATGCTAGACCAGTGCTTAGAACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026532:ENSMUST00000027817:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.235 A=NA C2=0.379
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(31.4=100)
A:
NA
C2:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAAAACCATTGGCGGTGTGA
R:
GGTGGCCGCTGTCTATAAGTT
Band lengths:
168-262
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