MmuINT0151685 @ mm10
Intron Retention
Gene
ENSMUSG00000026532 | Spta1
Description
spectrin alpha, erythrocytic 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:174244044-174245192:+
Coord C1 exon
chr1:174244044-174244231
Coord A exon
chr1:174244232-174245138
Coord C2 exon
chr1:174245139-174245192
Length
907 bp
Sequences
Splice sites
5' ss Seq
CAAGTACTG
5' ss Score
0.23
3' ss Seq
TATATATTTTTTTCTTCCAGAGA
3' ss Score
9.49
Exon sequences
Seq C1 exon
AGGAAACAGAAGGAGATCCAGGCAATGAAGCGCCATCTGACCAAGATTGAAGACCTGGGGGACAGCATGGAAGAGGCTCTGATCCTTGATATCAAATACAGCACCATTGGACTGGCCCAGCAATGGGATCAGCTGCACCAACTAGGGATGCGAATGCAACACAATTTGGAGCAACAGATTCAAGCCAA
Seq A exon
GTACTGGTTTAAACCCAGGGCAGGGAGTGGAGTAGATGGTGTTAGATGTTGGAGCTTAACTTGGTTGGGCTTCAGGCACCTGATAAAGAGCACTTACAGAGATGTTCCGTTAGCTTACCATATCAATCTCTCTTTTCTGTTCCACAACTGAGCTACTTTTCTTCATAGTAGGGTCCACTGTGAAATAAGCAATGCGTCTCTGCCTCTATGTGTACACATCTTCCTTAAAGACACATGAGTCCTCCATCCAATTTTCAGGGTCCCTTTAACATCGTATGATCTTTTCATTTTCAGAAACCATTCCCTTTTATAAACTTCCATTTAAGCTATAATATCTAAAATGGAAGATTCAAACTGTGGACTAATAAAGCATAAAGGAAGAAATTAATTTTTCCTAAATAAATTAAACCTAGCACAGCAGTTTATGTCTTAATAGTCTTTGAAACAATTTTTGTACATTCTAAATTGACGATCGTTTTCTCTAAATTTCCTTGTTATAAATAATTAAACCTTTTCAAACCATTAAATTTCTGTTGAAGCTTTGCAATTTTTGCTAATGTACTGGAAAGCAGCCAAGGAAAATTTGTAACTGAATGATCATGGCTCTGTTCCAATAAAGCTTTATTCATAGGCTTTGAATTTGAATTTTACACATTCTTCATGATTCATAAAACATTTTTTGATTGTTTTCAGCAATAAAGAAATGTTGAAACCATTCTTGTCACAGGAGCTGTTTAGAAACAGAAGGTGGCTAGATTTGGCTCCTGGAGCATAGCTTGGAAGCCTCTGAACCTAGATACCTCAAATAATATATTGTGCATTAAAATTCCTCTACCTTTGCTATGGCATGTCTTTTGACACTTACTGTTTTGTTTCCAGAGTTAATTTATATATTTTTTTCTTCCAG
Seq C2 exon
AGACACCATAGGTGTGAGTGAGGAGACATTGAAAGAATTTAGCACCACATACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026532:ENSMUST00000027817:48
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(55.9=90.5),PF134991=EF-hand_7=PU(1.2=1.6)
A:
NA
C2:
PF134991=EF-hand_7=FE(22.0=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:
GGAAACAGAAGGAGATCCAGGC
R:
TGTATGTGGTGCTAAATTCTTTCAA
Band lengths:
240-1147
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