RnoINT0143037 @ rn6
Intron Retention
Gene
ENSRNOG00000015396 | Sptan1
Description
spectrin, alpha, non-erythrocytic 1 [Source:RGD Symbol;Acc:621714]
Coordinates
chr3:8555233-8555607:+
Coord C1 exon
chr3:8555233-8555366
Coord A exon
chr3:8555367-8555462
Coord C2 exon
chr3:8555463-8555607
Length
96 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTA
5' ss Score
7.64
3' ss Seq
GACTGGTTCCTCTTCTGCAGGGA
3' ss Score
8.95
Exon sequences
Seq C1 exon
GAGCAGCACCCGGAAGAGGAGCTGATCAAGACCAAGCAGGAGGAGGTGAATGCAGCTTGGCAGCGACTGAAAGGCCTGGCTCTTCAAAGGCAGGGGAAGCTCTTTGGTGCTGCCGAGGTTCAGCGCTTTAACAG
Seq A exon
GTACTAGGGCTGTGAGCACAGGGTAGAGCGTGGACTCTGGTGTCCCAGTGCTCCTGAATAGCTGCATACCTGAGTTGACTGGTTCCTCTTCTGCAG
Seq C2 exon
GGATGTAGATGAGACCATTGGTTGGATTAAGGAGAAAGAGCAGTTAATGGCCTCTGATGACTTTGGCAGAGACTTAGCAAGTGTTCAAGCTCTGCTTCGGAAGCATGAGGGTCTGGAGAGAGATCTTGCTGCTCTAGAGGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015396:ENSRNOT00000045827:6
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=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(32.7=75.6),PF0043516=Spectrin=PU(6.7=15.6)
A:
NA
C2:
PF0043516=Spectrin=FE(45.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAAGCAGGAGGAGGTGAAT
R:
CTGCCAAAGTCATCAGAGGCC
Band lengths:
173-269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]