MmuINT0151655 @ mm10
Intron Retention
Gene
ENSMUSG00000026532 | Spta1
Description
spectrin alpha, erythrocytic 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:174203253-174205408:+
Coord C1 exon
chr1:174203253-174203345
Coord A exon
chr1:174203346-174205270
Coord C2 exon
chr1:174205271-174205408
Length
1925 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GCTTGTTTGTTTTCCCCCAGCAA
3' ss Score
7.94
Exon sequences
Seq C1 exon
GCCCTTCTCAAGAAGCATGAAGCCTTCCTGGTGGATCTGAATGCATTTGAAAACAGCATAAAGGCTCTAAGAGATCAGGCAGAAGTCTGCCAG
Seq A exon
GTGAGAAGGGTCAGGTTCTGACAGTAATCCCACTTCTTAGTATAGATGTAAAGGGATTCTGTAACTGGCTTCTCTTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCCTTCCCTTCCCTTCCTTTCCTCTCCCTTCCTCTCCCCTCCCTTCCTCTCCCCTCCCTTCCTCTCCCCTCTCCTCCTCTCCCCTCCCCTCCTCACTCCTCCCCTCCCCTCCCCTCTCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTTCTCTCTCTTTTCTCTCTACCTCTTCCCCCCATCTCTTTCTTTCTCTCTATACAAACTAGGAAACAATGGCCAAGAAAACACTATTTCCATTATTATTTTTAAGGTGAGAATGTTAAACTCTTTGTAGCACCTATAATAAATGTAAGCCAAAATAAAATTTCAATAAGCATTAGGTTTGTTGATATACTTTATGGCTTTCTCATTTGCTCTTTTTTATCTTTCCCCTCTTATGTTTATAACTTTCATATTTTATCATCTTAATTTCTCTGCTTTGTGACTTGGATATTATTTAAACATCAAGATTTATCAAATAGAGAGATACAGGTTTGAATTAAAATAACCATGTCAGAAAATTAGCTGGTTACAGGGATGGAAATATTTTTACACATTTATATAAAGCACGTAGAAAATGGGACCATCATAAAAAAGTAATTTCTGTTCTCCTGAAATGACTGCCAGAGAAGAGAAACAATTTTATAATCAAGATGTAGAAAGACCCCTTGACAACTCATAATCCATGGAAACAGATGTACCAAGGTACAGAACCATCAAGCTTATTTGGGAAATCAGAAACATGTTTGGCTGAAAGTGTTGGAAGGCTAAGAAGTGGGTGATTCAGAGTGATTAACTTGGAATTAAGTAAGTGAAAAAGTACCTTATATATAGGGGAACAAGCCAAAGGAGATGTGTCCTTTTCTGCTTAAGGAATCATTCTAATGAGCGATTGAGAAACCACACTCTCAGTCTAGAATAGACTGAGCATGGCAAGTCAAAACAGGCTTACAGCACATCTGTTTGCACCTGTGTCAGAATGTGCCCAGTGGGTCCCTGGATACAGTCATGAGGCAATGCAACAGGTGACAGACATAAGTCAGAGAGCCAGAAAAGGAGGTTTCATCATCTACACCAGCCTGAATGGTGTGTGCTTTGGAGACAAAAACAAAACTTCACAAAAATTAAAAAAGAATGCATATCCTGGAACAGAGTGATTTCTTTAAAGAGAGAGAAATCTTACGTAGTATACTCGTAGTTTTTCGAATTCTGTGGCTTTTTCTGTGCTATAGGTTGTCAGTCTCTAAAGCACAAATTTCACAACCCCTTAATAAAATGAATTAAAGAGGAAGCAGACGGGGAAACTTGTTAGTAAAGGTCCAGAGAAAGCAGAGATAGGAGAACGTGATGACAGATGTGATGACAGATGGTGAGCCTCGTGTTCTCAGGTTCCTGAAATGTTGATGGGTGTGGTCTATTTGAATCTTCACAGAGAAGTATATTACCCTTCCCACTAAAGAACAGTAGTCTGGAACATACAATTCTTTCGATAGAATGTGCATGTGCTGTTGGCCATGTTCATTCTTCCAAATCTACCAGGTCTGTGATAGGTACTTCTGTCACTACGTACTGAAGGATCACAACTGTTAGGCTGCAGCCACATCAGAACTCCAGCCAAGGCTTCCCTCTCATGAGAGGCCCTGGAAACTGTGCACCACTAGTGAGATCTACATGGAAAGACTTTCAGGGTGCAACTGACATCTGGCTTGTTTGTTTTCCCCCAG
Seq C2 exon
CAACAGCAGGCAGCACCAGTGGACGAGGCTGGTCGAGAAGCTAGGGTCATAGCTTTGTATGACTTTGAGGCTCGCAGCCGTAGAGAGGTCAGCATGAAGAAGAATGATGTCTTAACTCTGCTCAGTTCCATCAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026532:ENSMUST00000027817:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.065 A=NA C2=0.130
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(34.9=100)
A:
NA
C2:
PF0043516=Spectrin=PD(19.8=37.0),PF0001823=SH3_1=PU(63.0=63.0)
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:
TGAAGCCTTCCTGGTGGATCT
R:
CTTGTTGATGGAACTGAGCAGAGT
Band lengths:
214-2139
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