RnoINT0132943 @ rn6
Intron Retention
Gene
ENSRNOG00000016254 | Sema4c
Description
semaphorin 4C [Source:RGD Symbol;Acc:1562837]
Coordinates
chr9:43133063-43133706:-
Coord C1 exon
chr9:43133531-43133706
Coord A exon
chr9:43133208-43133530
Coord C2 exon
chr9:43133063-43133207
Length
323 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGC
5' ss Score
7.14
3' ss Seq
CCAAGGCCCTTCTTTAACAGGGG
3' ss Score
6.08
Exon sequences
Seq C1 exon
GGTGACATGGGGGGAGCACGGACCCTGCAGAAGAAGTGGACAACGTTCCTGAAAGCTCGGTTGGTGTGCTCAGCCCCGGATTGGAAGGTCTACTTCAACCAGCTGCGGGCAGTGCACACCCTGCTGGGCGCCTCCTGGCACAACACCACCTTCTTCGCGGTTTTTCAAGCTCGATG
Seq A exon
GTATGCTGTGCCACTGTGGGGTAGCTGGGGGGTGGGGAGGAGCAGGTGGTCAGGTCAGGTAGGGATGGTGTGTGGGTGTGAGGGCCCCCTCACCAGGCGTCTGGAGGAAGTCCAGCGGGTCAGTGCCTGGCAGCCAAGCTGCCTTTGTGCCTGCTCTTTTTAAAGCTCTGTGGGGGAAGGTGAGCAGAACCCTGCCTTGATACCTCAGAGCTACCTCATGGTCCTGACTGCTCCATATACCAAGCCTTGCTTTTTCCTCTGGAGCTGGGTATGGTGAGGGTAAGTAGGCACGTGACCTGACTGCCAAGGCCCTTCTTTAACAG
Seq C2 exon
GGGTGATATGGACCTGTCAGCAGTCTGCGAGTACCAGTTGGAACATATCCAGCAGGTGTTTGAGGGTCCCTTCAAGGAGTACAGCGAGCAAGCCCAGAAGTGGGCCCGCTATACTGACCCAGTACCCACCCCCCGGCCCGGTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016254:ENSRNOT00000021956:10
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(13.5=100)
A:
NA
C2:
PF0140314=Sema=FE(11.2=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:
GAGCACGGACCCTGCAGAA
R:
GGGTGGGTACTGGGTCAGTAT
Band lengths:
294-617
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]