RnoINT0142991 @ rn6
Intron Retention
Gene
ENSRNOG00000015396 | Sptan1
Description
spectrin, alpha, non-erythrocytic 1 [Source:RGD Symbol;Acc:621714]
Coordinates
chr3:8563624-8564186:+
Coord C1 exon
chr3:8563624-8563779
Coord A exon
chr3:8563780-8563981
Coord C2 exon
chr3:8563982-8564186
Length
202 bp
Sequences
Splice sites
5' ss Seq
AAAGTAATG
5' ss Score
1.16
3' ss Seq
CTTCTCCTTTTGATTCGCAGGAT
3' ss Score
10.11
Exon sequences
Seq C1 exon
CTCCTGAGCCGCCGCAATGCCCTCCATGAGCGAGCCATGCATCGCCGGGCACAGCTGGCCGATTCCTTCCACCTGCAGCAGTTCTTCCGCGATTCCGATGAGCTCAAAAGTTGGGTCAATGAGAAGATGAAAACGGCCACTGATGAAGCTTACAAA
Seq A exon
GTAATGATCAATGTGTCCTGTAGTACCTGTGTAGTAAGCTAAGTCCCCTTGCAAAAACCGTTTGGAGCTAAAAACAAAACAAAACTAAAACCACAGAGAGTCACGCAAACCACATTAGTCATAGATTGTCTGTTTTATGACTGTGAAGTAGCTCTGTATATCCGAGTTGAAGGCACAACCCTCTTCTCCTTTTGATTCGCAG
Seq C2 exon
GATCCGTCCAACCTGCAAGGGAAAGTCCAAAAGCACCAGGCTTTTGAGGCTGAGCTCTCAGCCAACCAGAGCCGTATTGATGCCCTAGAGAAAGCTGGGCAAAAACTAATAGATGTGAACCACTATGCCAAGGAAGAAGTAGCAGCTCGGATGAATGAGGTCATCAGTTTGTGGAAGAAACTTCTAGAGGCCACAGAACTGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015396:ENSRNOT00000045827:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.135 A=NA C2=0.159
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(19.0=38.5),PF0043516=Spectrin=PU(27.9=55.8)
A:
NA
C2:
PF0043516=Spectrin=FE(65.4=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:
CAATGCCCTCCATGAGCGAG
R:
GACCTCATTCATCCGAGCTGC
Band lengths:
304-506
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]