MmuINT0151684 @ mm10
Intron Retention
Gene
ENSMUSG00000026532 | Spta1
Description
spectrin alpha, erythrocytic 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:174243148-174244231:+
Coord C1 exon
chr1:174243148-174243199
Coord A exon
chr1:174243200-174244043
Coord C2 exon
chr1:174244044-174244231
Length
844 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TTGACTTCCTCTTTTCCCAGAGG
3' ss Score
8.96
Exon sequences
Seq C1 exon
ATCATTGCTCAAGGAAACAGGAACTCTGGAATCCCAACTTGAAGCAAATAAA
Seq A exon
GTAAGTAATGTTTTTTTCACTAGCTGAAGACACTGCTTGGAATTTTAAAAGCACAGGGAAAAATACATAGAGGCAGCCTGGGGATGTTTTATGTAGAAGTTACCCTAGGATGTAGTTATACTCACATGTCAATTTGTATTCTCACTTCAGATCCTGATATTATACAGGCCCCAGTTTACTTACATCTTTGAGTATAAGCTTTTACAATACATCTAAGCTAATGAATACATGAAAGGTACTTAACTGTAAGAGCAGATACTCATGTTCCTAACCTATAACCTAGAGTATCAATAAATTTCTATTGTTTGATATAGGCAAGTGATATAACAGGATGTAGATCCGCTCATTTCAACTAAGGGAAACAGTGCTTTAGAGGGGTATTTCTCAGTCTTGTTTGCATTATTGTCTTTCTAAGATTAAAAAAATATTTAGTTCAATATACATTTTCACTAATGAGAAAAGAATAAGATGTCAGAATAATCTACTCTGTAACATCAAAGTGTCTACCCATCCCTCAGAGCCACTTTGCCCATTGATGTGAGATGAACAACTTTCCCTTGTTGGAATGCTTTGGGAAAATGTAGACTTTTTTACACATGTATACTATTGCTTAGACAGATGCCTGTCATCGCTGATGGTGAAGGAGTCTTGGAAATGGACACACTGAGGCTATTGCATGAGTCAGAGAGCTAATTCCTAGTGAATGAAGATAATTCACAGTGTGCTAACTGGAGCTGGTGGGGTCTGAGTTCCAGGATGACAACCATCATCTCACAGCTGTTTTTCAAAGGGAGGATTAAGAAGGGTTGTAACTGGTGAGTCGATTGACTTCCTCTTTTCCCAG
Seq C2 exon
AGGAAACAGAAGGAGATCCAGGCAATGAAGCGCCATCTGACCAAGATTGAAGACCTGGGGGACAGCATGGAAGAGGCTCTGATCCTTGATATCAAATACAGCACCATTGGACTGGCCCAGCAATGGGATCAGCTGCACCAACTAGGGATGCGAATGCAACACAATTTGGAGCAACAGATTCAAGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026532:ENSMUST00000027817:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.032
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(16.7=100)
A:
NA
C2:
PF0043516=Spectrin=PD(55.9=90.5),PF134991=EF-hand_7=PU(1.2=1.6)
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:
TCATTGCTCAAGGAAACAGGAACT
R:
TGGCTTGAATCTGTTGCTCCA
Band lengths:
238-1082
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