RnoINT0132920 @ rn6
Intron Retention
Gene
ENSRNOG00000019737 | Sema4a
Description
semaphorin 4A [Source:RGD Symbol;Acc:1304636]
Coordinates
chr2:187813163-187813588:-
Coord C1 exon
chr2:187813490-187813588
Coord A exon
chr2:187813269-187813489
Coord C2 exon
chr2:187813163-187813268
Length
221 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
CAGCCTCTTCCCCCCTCTAGGAA
3' ss Score
11.03
Exon sequences
Seq C1 exon
ACACAGTGTTTCAACTTCATTCGTGTGCTGGTCTCTTACAATGCCACTCACCTCTATGCCTGCGGGACTTTTGCCTTCAGCCCCGCCTGCACCTTCATT
Seq A exon
GTGAGTAGTCGGATACTCCGCTTGCTCACAGCGCCCCTCCCCCCACCTCTCTTCACACCCACCCCAGCCTGTCCTCCGAAGGTTTGGGAATCTCTGGTCCCTGAGGAAGATTCCTAGCCCCAGACCAATTTCCCTCTCTGTCCCTTTTACTTCCTCATGCTCCTCATCTCTCAGACGTGCGACCCTGGCATTCTGGGCTCCCAGCCTCTTCCCCCCTCTAG
Seq C2 exon
GAACTCCAAGATTCCTTCCTGTTGCCCATCTTGAAGGACAAGGTCACAGATGGGAAGGGTCAAAGCCCCTTTGACCCTGCTCACAAGCACACAGCTGTCTTGGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019737:ENSRNOT00000056862:5
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=0.041
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(32.3=100)
A:
NA
C2:
PF0140314=Sema=FE(19.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACAGTGTTTCAACTTCATTCGTGT
R:
CGACCAAGACAGCTGTGTGC
Band lengths:
204-425
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]