RnoINT0142957 @ rn6
Intron Retention
Gene
ENSRNOG00000003537 | Spta1
Description
spectrin, alpha, erythrocytic 1 [Source:RGD Symbol;Acc:1305194]
Coordinates
chr13:92298797-92299197:+
Coord C1 exon
chr13:92298797-92298896
Coord A exon
chr13:92298897-92298999
Coord C2 exon
chr13:92299000-92299197
Length
103 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
CCTCTCCTACTTTCCCACAGGAG
3' ss Score
11.47
Exon sequences
Seq C1 exon
TGATCTAGAGAATTGGATCAAGGCCATTGGTGGTGTAATATCATCACCTGAGCTGGCTGAGGACTTAACTGGCACAGAGATCTTGCTGGAGCGACACCAG
Seq A exon
GTACAGCTACACAGTCCACAGCCACTGCGCAGTGATGTAAAACTCTCTTCTCACTGCAGAAGGTTCTATAATCTTCACTAGCCCCTCTCCTACTTTCCCACAG
Seq C2 exon
GAGCATTATGATGACATAAAAAGAGAAGACCCCACTTTCCAAGCCTTAGAAGACTTTGGTAGAGAACTTATAGACAGAGGCCACCGTAATAGCCACGAAATTGAAACTACTCTCCAGGATATTAAATTAAAGAGAGACGATTTGGAAAAGAATTGGGAAAACCGCAAGAAGATGCTAGACCAGTGCCTAGAACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003537:ENSRNOT00000004716:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.059 A=NA C2=0.136
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(31.4=100)
A:
NA
C2:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTGAGGACTTAACTGGCAC
R:
TGCAGTTCTAGGCACTGGTCT
Band lengths:
243-346
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]