RnoINT0132955 @ rn6
Intron Retention
Gene
ENSRNOG00000016254 | Sema4c
Description
semaphorin 4C [Source:RGD Symbol;Acc:1562837]
Coordinates
chr9:43133791-43134152:-
Coord C1 exon
chr9:43134036-43134152
Coord A exon
chr9:43133943-43134035
Coord C2 exon
chr9:43133791-43133942
Length
93 bp
Sequences
Splice sites
5' ss Seq
ATGGTTAGT
5' ss Score
7.07
3' ss Seq
CCTCCTTGCTTTGTCCCCAGAAC
3' ss Score
11.3
Exon sequences
Seq C1 exon
ATGGTGAACTGTACTCGGCTACACTCAATAACTTCCTGGGCACAGAGCCGGTTATCCTTCGAAACATGGGGCCCCACCACCCCATCAAGACGGAGTACCTGGCTTTTTGGTTGAATG
Seq A exon
GTTAGTCACGGAACAGGATTGGGGAAGGCCTGAGTGGAAGGGTCTTCAAGGGCCCTGGGACTCTGCCACTGACCCTCCTTGCTTTGTCCCCAG
Seq C2 exon
AACCTCACTTTGTAGGCTCTGCCTTTGTCCCTGAGAGTGTGGGAAGCTTCACGGGAGATGATGACAAGATCTACTTCTTCTTCAGTGAGCGGGCAGTGGAGTATGACTGCTACTCCGAGCAGGTGGTGGCTCGAGTGGCACGAGTCTGTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016254:ENSRNOT00000021956:8
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(9.1=100)
A:
NA
C2:
PF0140314=Sema=FE(11.7=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:
ACAGAGCCGGTTATCCTTCGA
R:
GCCCGCTCACTGAAGAAGAAG
Band lengths:
170-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]