RnoINT0133053 @ rn6
Intron Retention
Gene
ENSRNOG00000004033 | Sema6a
Description
semaphorin 6A [Source:RGD Symbol;Acc:1305493]
Coordinates
chr18:41375161-41377354:-
Coord C1 exon
chr18:41377264-41377354
Coord A exon
chr18:41375281-41377263
Coord C2 exon
chr18:41375161-41375280
Length
1983 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
TCCCTCCTTTTTCTCCTAAGATG
3' ss Score
8.85
Exon sequences
Seq C1 exon
GTGGATACTTTGGAAACTTTTGGGGATGAATTTAGTGGAATGGCCAGATGCCCTTATGATGCCAAACATGCCAACATCGCTCTGTTTGCAG
Seq A exon
GTAAATGGCCTGATTTCTTCTCATTACGTTTGTTTTTGCGTCTTTCAGCTGAGAATTCGCTGGGAAGGAATTGTACTGACTCTCTGGTGAACACTGTAATTAGGAATGCCTTTCATTTGAAATCAGGATGGGAAACCAAGTAGTTTTGCTTCTTTACAGAGTCTCTGTCCCACCCGCACAGGCTTCTGTGCCTTCAGGAAAGTTTGACAGCACAGCACTGCATGGGTGAAGACAACTTCAGGCTCAGATACTAGAAAACCTTATGTACTAGAAAACCAGCCACCAATGCAGATTTAATGCTTGCGGTCAGGTTGACTTGGACTCAGCAGTGTCCCTCCTAGCCTTTTCCCTGTTCTCTACTACCTTCTTTATGAGACAGCTGTTCTCACAACCTCAAAGGCTACACATGGAGCAAGAGGGAGAGAAGGAAAAGGAAGCTTCTGGATGCTTTTTCACAGCAGCCAAACAAGACTTCTCAAATGCCATTGATGTGAATTGGCTACAAGCATATCTCTGACCAAATGGCCACAGTGTCTGAAAAGATAGTGCTGATTGCCTAGGTGGGCCCAGGTTCCTGGTGAACTGGGTATGAAGCAGTAGTAGCTAAGAGGCCATCCTTTTCTTATTTAGTAGGGTTTTTGTATATGAGTAGGTTTTAATTGGGGAGTGTATTTAGGAAATCATTGCCAGCTGTGTGTGTGGAAGCGGATACAGAGAGAAGCGTTGGTGTGAAGGGATTGATTGCTCCAGCATGCAGTCACACCATCGGCTGCCATTCCCATCAGGACAGCAAACACCTGGCCTAGGCTAGCTCAGAAGGTAGCTTGTAGACAGGCATTTTCTATCTGTATATTTGTGCAGCAAATGCATGCCTGGTGCCTCTGGAGGCCTGAAAGGGGCATCAGATCCCATGGGACTAGAGTTACAGATGGCTGTGAGCTACAGTGTGGGTGCTGGAAATCAAAGTTGGGTCCTGAAAGGGCAGCCCGTGTTTTCCATTGCTCAGTGCTCTCACTATCTCCCACTCAGGTAAACTGTCTAAACTTTGAGTACACTTGATTTCTGTTCAGTTAACACAGTTCTTATTTTTCTTAACTATCTCGTTTGGTTTGGGGTTGCAGAATATTTGCTAATCCAGAAAAGAGACAGAAGTTCAGTGACTCACTTTCAGCTTTCTTTGCTGTCTTTGCTTTTGGACATGCCCTCGAGCTTGTCTCCCACAGCAGAGAATTTCTGAAGAAAGGCCGGTTTTTTTCTCAGCTCTCTCCACACCTTCATCCTTTGCTTTGGCCACTTGCACAGCACAGGGCTTCCATTTTGTGACTTTGGAAATCCAGAAGGAAAGGTCTGTTATTTAAGCTAGATTGGCAGGACTTACTGAATCACATGACTAAGGAAAAGAGACTGAGTCTTGGGACAAAAGAAGTCATCTGACTAAGGAAAAGAGACTGAGTCTTGGGACAAAAGAAGTCATCTGGTTAACCATTAGTCTTTGAACCCTCTCCGTTCATCCCACGCCGAGTCAGGCTTGGGCCATCCCTATTTCCGAATGGAATTAAAACCTGTGTTGATAAAAATCACTTTCTTGTTTCTCAGGGTTCCCTCCTAAGCCAAGTGACCATGGCGTGGTGGCGGCTGTAGCAGCGGCCAAGGGTCCTTGGCCTTGAGCTTGCAGTCAAGGTCCATGTAATCAAGTGAAGCAAATAGCATATTTCATTTGCCCTGTTCCCTGAGCTGCTGCGGCTGCCACTGCTGCTTAGGAAAAATTGCTGTGCAATTTAAAAACGAAAAATGTTTCATTTCTCGTGATCCTAATTCAAAATGGGGGGGGGGGCGCAAGCTTTTTCCTAGCGACTCTTGAATGTTTCCCAGTTGTCCTATCTCATTTGCCTGATGCCTGAAAGCAGACTGGGGGATGTCTTTGCTGTCCCCAGTCCCCGCCTTGCTCAGTACCCTGTTCAACTCCCTCCTTTTTCTCCTAAG
Seq C2 exon
ATGGGAAACTGTACTCGGCCACAGTGACTGACTTTCTGGCCATTGATGCGGTCATTTACAGGAGCCTTGGAGACAGTCCTACCCTCAGGACTGTCAAGCATGATTCAAAGTGGTTGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004033:ENSRNOT00000005446:6
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(6.9=100)
A:
NA
C2:
PF0140314=Sema=FE(9.2=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:
TGGATACTTTGGAAACTTTTGGGGA
R:
CAACCACTTTGAATCATGCTTGACA
Band lengths:
206-2189
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]