MmuINT0151664 @ mm10
Intron Retention
Gene
ENSMUSG00000026532 | Spta1
Description
spectrin alpha, erythrocytic 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:174214056-174215621:+
Coord C1 exon
chr1:174214056-174214253
Coord A exon
chr1:174214254-174215477
Coord C2 exon
chr1:174215478-174215621
Length
1224 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAG
5' ss Score
8.73
3' ss Seq
CCCCCCCCACACACACACAGTTA
3' ss Score
3.41
Exon sequences
Seq C1 exon
GAGCATCACGATGACATAAAGAGAGAGGACCCTACCTTCCAGGCCTTAGAAGACTTTGGTACAGAACTTATAGACAGCGGCCACCGTAACAGACGTGAAATTGACAATACTCTCCAGAATATTAATTCAAAGAGAGACAATTTGGAAAAGAGTTGGGAAAACCGCAAGAAGATGCTAGACCAGTGCTTAGAACTGCAG
Seq A exon
GTATAGCAACTTCTGGAGAATTGGGGGTTAGCCTTAGTTACCTGAGTGCTTAGAACTGCAGGTATAGCAACTTCTGGAGAGTTGGGGGTTAGCCTTAGTTACTTGAGTGCTTAGAACTGCAGGTATAGCAACTTCTGGAGAATTGGGGGTTAGCCTTAGTTACTTGAGTATGGTTTTATTTGCTGGTTGGGAGCATTCACTGTATCAGACTGTGTGAGCTGTAAACAGCGGGGCCTTGCGATTGCCTGGCACTGTGCTCTGAGTTATAGACTGAGCATCCTTGTGTTCTGTGATCTTGTTCCTGTTAAAGGAGACAGCAAGCGACAGTGAAATGGCTCAGTGGGCAAAGCAATTTGCTGAAAAAAAAGAAAAGCAGGATGAGCTGAGTTTCATCCCAGAACACACGGAGAAAAGGGAGACAACGCCACATAATTTCCCCCTGACTTTCCCATGCATACCACAGATACCCCACACACACCTACCCTTTCTTGCATACACAAACAGGCATACTACTAAAAAACTGATAAATATTGATTTTAAAATTAAAAGCTTTTTTAAAGGAGAGAACAAAACGAGATTGTAATCATCTTGTACATTAATGGAATTATTGGCATTATTATTAAGTAATTAACTGAAGGATTTGTTTTCATGAAGAATAGCAATGAAGGTCACAATTCTATGAATATCATTACAATAGGAGATGTTTACTAACAGAATATAATGTATGAATCCGCTAAGGATAAAAAAAGGAGTGATCACAGTGTGTGATGAAAGAATATGGATATATTACACACATCTAATACTGTACAAAGTTCTAAAGAAGTTACCTGCGGAAAATCAGACACACGTAGATCAAGCTGCATACTGAATTTGTTGCCATCACAAACTAGCCAAAACTATGTCTCTACTTGAGAGAGACAGAGACAGAGAGAGAGAGAGAGACTAAACCAGTTCCTATCTACTATATCTACTAGATGAATACCGTACACTGGCAGTATCTTCACATTTACTATAGCTCATAGAACACATGGTATCTTTAAAGCAAACAGTGAAGTGACAAGGTACTTGAGATTCATTCTAAGAATGCCGTGGGAGAGGATGTAACATCCCTGGCAGGATGTTTTGTGTCATCACAATGAGGAAGGGTAAGATCAGTTCCTTCGCCCATCTAGAATTACCACATGCCTGCCTCTGATTTCACCTACCCCCCCCACACACACACAG
Seq C2 exon
TTATTCCGAGGAAAGTGTGACCAGGTCGAGAGCTGGATGGTGGCCCGTGAGAATTCCCTGAGGTCAGACGACAGGGATCACTTAAACAGTCTGCAGGCTTTGATGAAGAAACGGGATGATTTGGACAAAGCAATCACTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026532:ENSMUST00000027817:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.379 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
A:
NA
C2:
PF0043516=Spectrin=FE(45.2=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:
GAGCATCACGATGACATAAAGAGAGA
R:
TGATTGCTTTGTCCAAATCATCCC
Band lengths:
334-1558
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