MmuINT0151647 @ mm10
Intron Retention
Gene
ENSMUSG00000026532 | Spta1
Description
spectrin alpha, erythrocytic 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:174192920-174193684:+
Coord C1 exon
chr1:174192920-174192997
Coord A exon
chr1:174192998-174193528
Coord C2 exon
chr1:174193529-174193684
Length
531 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGC
5' ss Score
6.16
3' ss Seq
TGTGTGTGTGCGCTTTACAGCTT
3' ss Score
9.56
Exon sequences
Seq C1 exon
ACCTTGGATGAGACTGCAACCAAGCTTATTGACAATGACCACTATGACTCTGAGAATATCGCTGCTATTCGTGATGGG
Seq A exon
GTATGCCAAGGGCCAGAGCCTCTCTCTACCTGTCCGTCCATCTCGGTGGCTGTAATAAAACACTGATGAGAAGCAACTTGGGGGAGGAAAGGGATTATTTATCTTTCGGGTTTGCAATCTATTATAAAGGAAAGCCAAGTCAGGAACCTGGTGTCAGGAACGGAAGCAGAGACCATAGAGGAATCCTGCTTACTAACCTGATCCTCATGGCTTGCACCACCTGATATTGCCCACCATGCTCCGTCTTATATCAGTCATTAATCAAGAAAATGTTCCCACAAACATCCCCACAGGTCAATCTTATGGAAGCAGTTCTTGAATTGAAGTTTGATCCTCCCAGATGACTCTAGTATTTACAAGTCAAGTCATGGCCTGTGCACCAGTATCAGGAAAAGCATTGGGGAAAGACAGCCAGGGTGGGCAGTGATCTCAACTGTCTATATTTGCTTTTGATGGCCATGAGTTTATTTACAGTTCCATGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCTTTACAG
Seq C2 exon
CTTTTGGCCAGACGTGATGCCCTGCGTGAAAGGGCTGCCACTAGAAGAAAATTGTTGGTAGATTCACAACTTCTTCAACAACTGTATCAAGACTCAGATGACCTAAAAACCTGGATCAATAAGAAGAAAAAGTTGGCTGATGATGACGATTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026532:ENSMUST00000027817:13
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:
PF0043516=Spectrin=FE(23.8=100)
A:
NA
C2:
PF0043516=Spectrin=PD(19.0=38.5),PF0043516=Spectrin=PU(27.9=55.8)
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:
TGGATGAGACTGCAACCAAGC
R:
CTTGTAATCGTCATCATCAGCCA
Band lengths:
230-761
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