MmuINT0151689 @ mm9
Intron Retention
Gene
ENSMUSG00000026532 | Spna1
Description
spectrin alpha 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:176176605-176178580:+
Coord C1 exon
chr1:176176605-176176749
Coord A exon
chr1:176176750-176177462
Coord C2 exon
chr1:176177463-176178580
Length
713 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
TCTCCTTTCATTCTTTCCAGGCT
3' ss Score
11.3
Exon sequences
Seq C1 exon
GAAAGGATATGTTTCACTGGAAGACTATACATCATTCCTGATTGACAAGGAGTCAGAGAATATCAAGACCAGCGATGACATAGAGAGTGCATTCCAAGCTCTGGCAGAAGGCAAGGCCTATATTACCAAGGAGGACATGAAACAG
Seq A exon
GTGGGATTCCCACTCTTGCTTCTCCTATTCTGACACTGTAACCTTGGTTTGGGTCATCTTGGTCTCCGCTCTCCTCCAGGAGCTCCCACTCGAATACCCACTGTATTACCTCAGGCCTCCTCTTTCACAAGGTATTACTTATTTCAGTAAATCATTTGTCTTACTCCAGCCCTAGCCCCAAATATCTACTTGTTCTCTACTGACTATTACAGTCTGTTCGAAACATGCAACTCAATTTTTAAGCAGTCTGTTGCCATTTCTACTTAATAAGCCAAATTGAAGAAATAGAAAGACCTAATTTTTTGATGTTGAATATTGAAAAGTGAAAGAGGGTTTGAAGGGGACATGGAAACTATCAAAGCACATATGACATATAAAATGGACAGAGGAATGCTAGGGATATAGAACAAGAAGGGAGTATGTGAAAAAGAAATGGGGGATTGAGAGATCAACAAAATCAAATTGTGTTTGAAATACCATAATGACATAAGATGTGTGCTTGTTTTGGGTTTGTTTTTTTCTCAAAAACATCTAAAGAAAAGGATATGAAAAAAAGACTCAGGAAGAAATTTGAATTTTTTATTCATTCGATGGAATAAACTTATGGAAACTCAGAGTGATAGGCAGAAAGCTGCTTCTTCTGATGGCTCTCCATCTGTGAGAACAAGTGTTGGGTTTCTGTAACTCTGTCTTTCTCCTTTCATTCTTTCCAG
Seq C2 exon
GCTCTCACCCCGGAACAAGTGTCATTCTGTACCATACATATGCAGCAATATATGGATCCACGGGGTCGGAGCCAACCTGCTGGCTACGACTATGTTGGCTTCACCAATTCATTCTTTGGCAATTGATATGCAGATTCTTATGCATCATAGAAAATCATAGTGTGGCAGCAAGTAATGGGGGATAAGAGGCACAAGCAAGCGTGAAAGAAAAAAAGATCCTGCTGCTCTGTGTGTGTGTGTGTTACATTTATTGTGGGATTTTTAAAAAAATAATCAAGTATATAGCGGGGGCTAAGAAAAATCTATAGGATTATGTAACTAGTCTCTACCTAGGGTGCCAAGATTTTAATGTGTGTGTGTGTGTGTGTGTATGTGTATGTGTGTGTGTGCTGCACACCTTTAAGATTTTACTGCATTCTGATTATAGCAGAAATATTTCTTTTTTAAAGGGAAATTTAGGTAAAATTATGCTTTTGTATTTTTGGAACCATATTATTACTAAATATAATATGCAATTAATTATACTGTGGAAAAGGACAATAATAAATTAGATAAATAAAATACAAGGTGATTCACAGTTTGTTAGTAGCTTTTAAGAGAGATGAAATCCTTACAATTTGAAATGTTTGTAATTTTGTCTTATTCTATGAAGTAGAGTCAGAAAAAGATAACATAAAATGCTTGTTTTCTTCTTGTCCTGTTTTGATATTTCACCATTAAAGTGAATGACTTTGGCATGTCAGGGTCCTCTCATGTTCCCTAAATCTCTGAATACTCTCTTACATTTTAATATGATACAACTGATGTTTTATTCATTTCTATCTTCTCAGAAGCCAGTAAAATGTTCATAATTTAAGGAAAAAACCAAGAAGCTATGGTGGTACTATATCTAGGTGTTTTCAGTACAGGTATGTTTCTTAGGTAACTTTGTTGCCTTTTGTGAAATTTAGCCTTTCGTACAGATAGCCTATTGCTCATGAATATCACTCCTTATTTACTATCTTAAGTCTCAGTTTTTTCGCTTGAGTAGAAATTAACCCCTCCTCAATCTTTGGGAAAAAATTCTCACAGGATCTAATTAAAATACTTATGGCTACAAATAAAGATATTTGAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026532-Spna1:NM_011465:51
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=PD(15.9=26.5),PF087265=EFhand_Ca_insen=PU(40.6=57.1)
A:
NA
C2:
PF087265=EFhand_Ca_insen=PD(56.5=92.9)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCATTCCAAGCTCTGGCAGAA
R:
AGCCCCCGCTATATACTTGAT
Band lengths:
350-1063
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: