MmuINT0151728 @ mm10
Intron Retention
Gene
ENSMUSG00000057738 | Sptan1
Description
spectrin alpha, non-erythrocytic 1 [Source:MGI Symbol;Acc:MGI:98386]
Coordinates
chr2:30018362-30020047:+
Coord C1 exon
chr2:30018362-30018570
Coord A exon
chr2:30018571-30019926
Coord C2 exon
chr2:30019927-30020047
Length
1356 bp
Sequences
Splice sites
5' ss Seq
CAAGTGCGT
5' ss Score
6.68
3' ss Seq
GCACTGCCCTTGTTCTGCAGGGA
3' ss Score
8.99
Exon sequences
Seq C1 exon
GATCGTCTGAAGGACCTGAACAGCCAGGCTGACAGCCTGATGACTAGCAGTGCCTTCGACACCTCCCAAGTGAAAGAGAAGCGGGACACCATCAATGGACGCTTCCAGAAGATCAAGAGCATGGCCACCTCCCGAAGAGCGAAACTGAGCGAGTCCCACCGCCTGCACCAGTTCTTCCGGGACATGGACGACGAGGAGTCCTGGATCAA
Seq A exon
GTGCGTGCTGGGCTCTGCACTTACATTCTCATTGTCTTCTCATGGGGCTGCCTGGAGAGCCGGGGGTCACAGGGAAGTGTGACGTGAGGGTACAGGATCATCCTGTGTGCTTTAACCATCATGTCACAGGAAGCCCTACCTTTTGCATCCCGAGGAAAGTTTTGATTTTTTTTTTTTTTTGAGTCAGGATCTCTATGTAGTCTGAGGGATCACTATGTAAACTAGCCTCTCCCTCCCAAATGCTTGCATTTAAAGGCATGTACAACCACTCCCGGCTTTTTTTTTTTTTTTTTCTCCCCATACCCTTAAAATTTAACCTTTTTCTATAGAGCAAGTTCCAGGGCATCCAAAGCTACACAGAGAAATCTTACCTTCAAGAACAAAAACAAAAATTCGGACATTTTATTTATTTCTTTTCAAATAATATGGCATATAAACAAGCCATTTCTTTTTATTGGCTTCCTTTTTTTTTGTTTGTTTTTGTTTTAAGGTTTGTTTGTTTTAGAGTTATCTCATGTAATCCAGGCTAGCCTCAATTTCATTGTGTAGCTCAATATTACCTTGAAACCCTAGGACTCTTGCTTCTACCTCATGAGTCTGTGACTATAGGTATGAACTACTATGTCTGACCTAAGCTATCCACTTTAAAAGAAAATCTCCTCCGTTAAAACCTTTTTTAAAAATTAAATGAGTTGGGGATGGAAAGATGGCTCTGGGTTGGATTCTCATCACACACCTGGAGGCTCACAGCCATCCATAACTCTAGTTCCAGAAGATTCAGCCCCTCTTCTGACCTCTGGGCACCAAGAATGTATGTGCATACATGAACGCAAAGCATTCATACATACAAAATAGATGAATCTTAGAAAACACCTTCTAACTTAAAAAAATACAGTACATGTGACCATCTTTTTTGTTTGATCGATTGGTTTTGGTTTTTTGAGGCAGTCTCTCTAAGTATCCCTGGCTGTCCTGGAACCAGACTGGCCTTGACCTCTACCTACCTCTGCCTTCCATGTGCAGGAGTTAAAGGCATGCACCACCACACCTGGGTTAAGGAGACATCTTTCTATGTTTTTCTCTGTATAACCCACAAGTAAGTGGAGTTAATAACTCCAGTGGTGCTCCTAATCCTCGGGGTAGGGCCTGTCGTCTGTAGACCCGTTCCATACAGATGAGCCTTGTTCATTGACAAATGTGCATGGCAGAGGCAGTTCTAGATCCATGGCTTTGGAAAACAGGCTTCTGGTTCTAGGAAATGGGTAGGAATTAGAGGATGCCAAGAATTAGTTGCTAAACTAACCTGGCCCCTGACATGAGCTGGTGTCAGCTGACTGCACTGCCCTTGTTCTGCAG
Seq C2 exon
GGAGAAGAAGTTGTTAGTGAGCTCTGAGGACTATGGCAGAGACCTCACTGGTGTTCAGAATCTGAGGAAGAAACACAAGCGGCTAGAAGCTGAACTGGCTGCACATGAACCCGCCATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057738:ENSMUST00000113717:40
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.157 A=NA C2=0.073
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(47.6=71.4),PF0043516=Spectrin=PU(16.2=24.3)
A:
NA
C2:
PF0043516=Spectrin=FE(38.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTCTGAAGGACCTGAACAGC
R:
CTGAATGGCGGGTTCATGTGC
Band lengths:
327-1683
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