MmuINT0151664 @ mm9
Intron Retention
Gene
ENSMUSG00000026532 | Spna1
Description
spectrin alpha 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:176144187-176145752:+
Coord C1 exon
chr1:176144187-176144384
Coord A exon
chr1:176144385-176145608
Coord C2 exon
chr1:176145609-176145752
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-Spna1:NM_011465:29
Average complexity
IR-S
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
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: