MmuINT0151678 @ mm10
Intron Retention
Gene
ENSMUSG00000026532 | Spta1
Description
spectrin alpha, erythrocytic 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:174230626-174231398:+
Coord C1 exon
chr1:174230626-174230788
Coord A exon
chr1:174230789-174231321
Coord C2 exon
chr1:174231322-174231398
Length
533 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGC
5' ss Score
7.53
3' ss Seq
ATTTTTTTCTTATTTGTTAGGTG
3' ss Score
8.81
Exon sequences
Seq C1 exon
GAAGAAACTCAGAACAAGGATAAGATTTCCACCAAGATCCAAGTTCTGAATGAAAAGACAGCCTCTTTGGCCAAGGCATTAGCTGCTTGGAAGTCACAACTGGACGATGTGCATGCCTTTCAGCAGTTTAACTGGAAGGCGGACGTAGTGGAATCCTGGATAG
Seq A exon
GTATGCGATGCCAGGGCTACTCTAAGAGTACCATTTGAAGAATGTCTCTAGATTTTTCCTTTACTTTTGGAAATGGGGTGAACTCATTTTTATTCCTCCTAGGCACAGTCTTACACACACACACACACACACACACACACACACACACACACACACACACACACAAATGTGCACACAGATGGTAGGGAATAAGGTGGCATAAACCCACAGGACAGTTGTTCCAAACTGGTAAATTTCATCATGCTATTCAGAAAGGAAAATCCTTCACAAAGTATTCTAGGAAACAAACTACAGTGTTTGTTGGTTGGTTTGTAGTTCATGTTCAACCTTCAACTTTCCTACCTCCCAGGATTCAACATTTCTTTTGCACTTAGCACTCTCAGTCAGTTTTATTTTAAGGGCAGAAAAGCCACCCACTCCTCCCATTGCTTCTGTATTGCACTGAGTCACCTGTTCTGGGATCAGGAAGCTTTCTGATTGGCTACTGTAAATAATCATCAAATATTCCATTCTATTTTTTTCTTATTTGTTAG
Seq C2 exon
GTGAGAAAGAAGCAAGCCTGAAGACCAAGAGCAACGGTGCAGACCTCACCGCCTTCCTCACACTACTGGCAAAGCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026532:ENSMUST00000027817:41
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.127 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(33.0=63.6),PF0043516=Spectrin=PU(16.0=30.9)
A:
NA
C2:
PF0043516=Spectrin=FE(23.6=100)
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:
GAAGAAACTCAGAACAAGGATAAGAT
R:
TGCTTTGCCAGTAGTGTGAGG
Band lengths:
239-772
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