RnoINT0143012 @ rn6
Intron Retention
Gene
ENSRNOG00000015396 | Sptan1
Description
spectrin, alpha, non-erythrocytic 1 [Source:RGD Symbol;Acc:621714]
Coordinates
chr3:8579669-8580096:+
Coord C1 exon
chr3:8579669-8579866
Coord A exon
chr3:8579867-8579949
Coord C2 exon
chr3:8579950-8580096
Length
83 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TCCACTCCTCCACTCTGTAGCTG
3' ss Score
7.26
Exon sequences
Seq C1 exon
GAACACCGGACAGAAATTGATGCCAGGGCTGGCACTTTCCAGGCATTTGAGCAGTTTGGGCAGCAGCTGTTGGCTCATGGGCACTATGCCAGCCCAGAGATCAAGGAGAAACTTGATATTCTTGACCAGGAGCGCACAGACCTGGAGAAGGCCTGGGTTCAGCGCAGAATGATGCTGGACCACTGCCTGGAGTTGCAG
Seq A exon
GTATGTACATAGCTCTGGCCGTTCTCTCATTTCTCAGAGTGGCCGCGTCTTCCTTCACACCTGTCCACTCCTCCACTCTGTAG
Seq C2 exon
CTGTTCCATCGAGACTGTGAGCAAGCAGAGAACTGGATGGCTGCCCGGGAAGCCTTCCTAAACACAGAAGACAAAGGAGACTCGCTGGACAGTGTGGAGGCTCTGATCAAAAAACATGAAGACTTCGACAAAGCTATCAATGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015396:ENSRNOT00000045827:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
A:
NA
C2:
PF0043516=Spectrin=FE(45.7=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:
CATTTGAGCAGTTTGGGCAGC
R:
TGCTTGCTCACAGTCTCGATG
Band lengths:
182-265
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]