MmuINT0151646 @ mm9
Intron Retention
Gene
ENSMUSG00000026532 | Spna1
Description
spectrin alpha 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:176121079-176123128:+
Coord C1 exon
chr1:176121079-176121189
Coord A exon
chr1:176121190-176123050
Coord C2 exon
chr1:176123051-176123128
Length
1861 bp
Sequences
Splice sites
5' ss Seq
ATAGTGAGT
5' ss Score
6.97
3' ss Seq
AAAAATGTTATTTTTTTCAGACC
3' ss Score
7.57
Exon sequences
Seq C1 exon
GCTTTCCTGGAAAATGAAGACCTGGGGAACTCAGTGGGCAGCGTGGAAGCCCTCCTTCAGAAGCATGATGACTTTGAAGAAGCGTTCACTGCCCAGGAAGAAAAGATCATA
Seq A exon
GTGAGTAAGGGCTCTGGTTGGACAATGATTTCCGAATTGTATGCACTGTCTCCATAAATCCCGCTAAAGTGAATCACCCTGTGACTATGAGACCTAACATGAGGACAGTTCCTTCTAAATTGCCACTGCTTGATTTGTTGTTGATAACGTTTAGCTACACATCTTAAAACACTGTGCTTTGATTCTGTGACCATATACAATATTTATATAGTGTGAAAGTGAAAACCAAGTCAAGATTCATCCTTTGGGGTCTGCAACCCTATAGGTGAATCAACAATATGAACTAACCAGTATCCCCTAGAGCTGTGTCTCTAGCTGCATATGTAGCAGAAGATGGCCTAGTCAGCCATCATTGGGAAAAGAGGCCCCTTGGTCTTGCAAACTTTATATGCCTCAGTACAGGGGAACACCAGGGCCAAGAAATGAGAGTGGGTGGGTAGGGGAGTGTGGTAGGAGGTATGGGGGACTTTTGGGATAGCATTTGAAATGTAAATGAAGAAAATACCTAAGGAAAAGAAAAAAAAGCCACTTGAACAGGTAGCAAGGTGACAATTGCTTACAAGAAAAATGAAATAAAAATGATACCTAATATCTGTAGTTCACAAATCTTAGCATATACATGACTTAGCATATACAAGACTTAGCACGTCTCTGTGTTAATAAAGTCTTTTGGATTCTGTCCTGAAAAAAAAAAAGATTCATCCTTTGGGGATAGAAAGGAAAATATTCACAGCAATAAAAAAAATATATTTTAACAATAAACTCCTTGATCTAGAAAATATATTTAGGAAGGTGATAGGACATAATTTCTTAGTTAAAAGAAATTACATACTTTATATTATGTGTTTTAAATTATAAATAAAATCCTATATTTAATAAAGAATCATCATGTAAATATTTGAAATATATTTGTCCTTTTCAGGAATACTTTAATGCATATTCCTCTCTAAAAATTTACATGTTCAATCGTAATTATTTTTATGAAGGATCATTTCCTTTATAATATATCTGCATTTTTATTTTTTATTTTTCTATCTAATGCAATTATGGAGCTTTACTTTGAAATTTAAGTTATAACATACTATAAAAATTTATCACCATATGAGGACTCTAAGAAAATGATACATCAGGGATGCAACTCACTGTCTGTCTTTGGTTGTCTCCTAGGGTAGAAAACACAGACACATGCAAGCACACACACACACAAAGACACACTTACTCACTCACACACAAGCATATACATCATCACCAACACTAGTTGTAGAAAACAATATAGTTGATTCCAAATCTCCCCTATTAATTAATATCAAACATAAGGTGAATCCTTATTAATTCATATACTTGTGTTAGATTCATACTGGCAAAAAGCTGAAATTAGAGTAACTCATTTTATTTTTTTACATATTTTGTATAATTTACCTATCCCAACTAATAAATCCATTGAGATATTTAGCAATTTGAGGGACTGATGAGCGAATATGGTTAAAAATTCACTTCTATATCACACTCAGTGTATCTAGGGACAGAGAGTAGCTGCAGGTAGATGGGATGGACAGAAGAGCTGTAAGAAAGTGACATTGGCTTTAATCCTTGATAGCGTTTCTCCTGCATTTACTCATAGTGACATCTGAATTCTTGTACTGTGACCTAGATTGAAAAAAATTATAGTGCAGAAAAGGCAATCATGTAGCCAAGAGTGTATATTTTAAGTTCAGGTATATCGGAACCCATAAGTAGGATCTAGGCCATCTAACCTTCAAAGTGTTGAAGTTGTACGTTGATATTGTTTGTTGTAAAGAGATACTCAAACTGGGGACACTCATTCAGCTGTTGCTGAGGAAAAAAATGTTATTTTTTTCAG
Seq C2 exon
ACCTTGGATGAGACTGCAACCAAGCTTATTGACAATGACCACTATGACTCTGAGAATATCGCTGCTATTCGTGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026532-Spna1:NM_011465:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(34.3=100)
A:
NA
C2:
PF0043516=Spectrin=FE(23.8=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:
CCTGGAAAATGAAGACCTGGGG
R:
CCCATCACGAATAGCAGCGAT
Band lengths:
184-2045
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: