RnoINT0142982 @ rn6
Intron Retention
Gene
ENSRNOG00000003537 | Spta1
Description
spectrin, alpha, erythrocytic 1 [Source:RGD Symbol;Acc:1305194]
Coordinates
chr13:92273003-92273850:+
Coord C1 exon
chr13:92273003-92273136
Coord A exon
chr13:92273137-92273705
Coord C2 exon
chr13:92273706-92273850
Length
569 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
CTCATGACTTTGTCTGCTAGGGA
3' ss Score
6.99
Exon sequences
Seq C1 exon
GAGCAACACCCTAAGTTGCCTGAGATAAAGGCAAAACAAGATGAAGTCAATGCTGCCTGGGATCGTCTCTGGAGCCTGGCTCTCAAGAGACGAGAAAGTCTATCAAATGCTGCAGACCTCCAGCGCTTTAAAAG
Seq A exon
GTATGGTACTGAAATTATAGCACAGTATGTAGATGGCTGACCTAATATACTGGAGGCCTGGCCTCTGATCCACATCACCACCTAAAGTAGGGAAGTAGAGGCAAAAAGACTATAATCCTAGGCATTCCAGTAGTAGAAGATCATGGGTGAAGATTACAAAATGTGTGGACTTAGCCACTGTTCACAGACTTCTATTGATAAAAAAAAGATAAGAAAAGAAAAAAGAAAATTAAAGCGTAGCACTTCTGAATTGAATTGGCTCTGAAGAAGTAAAGGGGGTATAAGAATTAGATGAGTTTGAGGGCAAGACTGGTATTCATGAATAACTTCTCACATGTCATATATGAGAACTGTCTCTGCAAGCTCAAAAGTCAAGAACCTTTGCAGTAGAACATCTCAGTGGAAAAATTCTGACACGGAAGAATGTTTTCAGTTACTTTGTGCTAGTTTGGTAAAAAGGAGAGTCGTTGCTACTTGAGGGAATTAAGTTGGTCCTATTGTGAGGGCTGTGGGTCTGTTTGCAATGTCTGCCATCTTGGTTTATTGATGCTCATGACTTTGTCTGCTAG
Seq C2 exon
GGATGTCAATGAAGCCATCCAGTGGATGGAGGAGAAGGAGCCTCTACTCACCTCTGAGGACTATGGCAAAGATCTTGTTAGTTCTGAGGCTCTGTTTCACAGTCACAAGAGGCTCGAGAGGAATCTTGCTGTCATGGATGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003537:ENSRNOT00000004716:6
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(33.3=77.8),PF0043516=Spectrin=PU(6.7=15.6)
A:
NA
C2:
PF0043516=Spectrin=FE(45.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAACACCCTAAGTTGCCTGAGA
R:
TCATCCATGACAGCAAGATTCCT
Band lengths:
272-841
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]