RnoINT0142941 @ rn6
Intron Retention
Gene
ENSRNOG00000003537 | Spta1
Description
spectrin, alpha, erythrocytic 1 [Source:RGD Symbol;Acc:1305194]
Coordinates
chr13:92280230-92281033:+
Coord C1 exon
chr13:92280230-92280307
Coord A exon
chr13:92280308-92280877
Coord C2 exon
chr13:92280878-92281033
Length
570 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGC
5' ss Score
6.16
3' ss Seq
TGTGTGTGTGTGTGTTACAGCTC
3' ss Score
11.43
Exon sequences
Seq C1 exon
ACCTTGGATGAGACTGCGACCAAGCTCATAGACAATGACCACTATGACTCCGAGAACATTGCTGCTATCCGTGATGGG
Seq A exon
GTATGCCAAGGCCAGAGCCTCTATCCGCCTGTCCTTTTCTGTTGGTGTGATGAAACGCTGACGAGAAACAACTTGGGGGAGGAAAGGGATTGTTTAGCTTTCAGTGCATAAGTTTTTATAAAGGAAAACCAAGTCAGAAGCCTGGCTTCAGGAACTGAAGCAGAGACCGTAGAGGGATGCTGCTTACTAACTTGACCCTCATGGCTTACACTACCTGACCCTGCTACCCTCAGTGGTTCATCTGACATGAATCATTAATCAAGAAAATGTTCCCCCAAACATCCCCACAGGTCAGTCTTATGGAATTGAAGTGATTTGAAGTTTGATCCTCCCAAATGACTCTAGTTTTTACATGTTGACTAAAACTGACCAACTTATGGCCTGTGCATCAGTATCAGGAAAAGCACTGGGGAAAGATGTCCACATTGGGCAGTGATCTCAACTACCTATATTTCCTTTTGTTGGCCATAAGTGTATTCACAGTTTAATGGTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTTACAG
Seq C2 exon
CTCCTGGCCAGACGTGATGCCCTGCGTGAAAGGGCTGCCACCAGAAGAAAATTGTTGGTAGATTCACAACTTCTCCAACAACTGTATCAAGACTCAGATGACCTAAAAACCTGGATCAATAAGAAGAAGAAGTTAGCTGATGATGAAGATTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003537:ENSRNOT00000004716:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(23.8=100)
A:
NA
C2:
PF0043516=Spectrin=PD(19.0=38.5),PF0043516=Spectrin=PU(27.9=55.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGGATGAGACTGCGACCAA
R:
TGTAATCTTCATCATCAGCTAACTTC
Band lengths:
230-800
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]