RnoINT0143025 @ rn6
Intron Retention
Gene
ENSRNOG00000015396 | Sptan1
Description
spectrin, alpha, non-erythrocytic 1 [Source:RGD Symbol;Acc:621714]
Coordinates
chr3:8592726-8593435:+
Coord C1 exon
chr3:8592726-8592885
Coord A exon
chr3:8592886-8593358
Coord C2 exon
chr3:8593359-8593435
Length
473 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
GGGGACACTTTGTTTTGCAGGTG
3' ss Score
7.4
Exon sequences
Seq C1 exon
AACAATCACCATGAGGAGAACATCTCTTCAAAGATGAAGGGTCTGAATGGTAAAGTGTCTGACCTGGAGAAAGCAGCAGCTCAGAGGAAAGCGAAGCTGGATGAGAACTCGGCCTTCCTTCAGTTCAATTGGAAGGCTGACGTGGTGGAGTCCTGGATTG
Seq A exon
GTGAGTGCGTGCAGAAAAGCCCAAAGCTTTGAGCTCTCCTAGGCTAAGCAGGTGGCAGAGCCACACAGTTGGTTTTGTGCTGTAGAGAAGAGACTGACAGGACATGGGCTCGGAGAGCGCTAAACACTGAGAGACACCCAGAGGTCAGAGCTGCCACAGCAGTGCCTACACCAGACTGGCATGAGGGTTCACCAAACAAGAGCCTGCAAACCTTGACACGAGCAAATACAAAGGCCCAAGTAGTCGTCGGCTCACCAAAGGGCCAGGTCGCATGAGGACTGCTCACCAGCTGCCCTGACCAGGGTGAACTAGATTCTGTTCTCAAGAGTCCTGGTGAGGCAGTGCAGAGAATAGACAGCTATGTGAGCTCAGGGAAGCCGCCAGTAACTCCGGAATGAATGTGTGAACGTTCCTCTGTTCCGTGGCTTGTTTCTTTGTCTGCCACTCTGCGAGGGGGACACTTTGTTTTGCAG
Seq C2 exon
GTGAAAAGGAGAACAGCTTGAAAACAGATGATTATGGCCGAGATCTGTCTTCTGTCCAAACTCTGCTCACCAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015396:ENSRNOT00000045827:45
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.296 A=NA C2=0.038
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(32.4=63.0),PF0043516=Spectrin=PU(16.0=31.5)
A:
NA
C2:
PF0043516=Spectrin=FE(23.6=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:
ACAATCACCATGAGGAGAACATCT
R:
TGGTGAGCAGAGTTTGGACAG
Band lengths:
231-704
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]