RnoINT0133080 @ rn6
Intron Retention
Gene
ENSRNOG00000021101 | Sema6c
Description
semaphorin 6C [Source:RGD Symbol;Acc:3659]
Coordinates
chr2:196337391-196337860:+
Coord C1 exon
chr2:196337391-196337505
Coord A exon
chr2:196337506-196337796
Coord C2 exon
chr2:196337797-196337860
Length
291 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAAA
5' ss Score
6
3' ss Seq
CCTCCTTACCTACCCTTCAGGGA
3' ss Score
9.93
Exon sequences
Seq C1 exon
GTACCTCTCCGTCATCCTGGTTCCGGGGCCTGGAGGACGATGCTGTGGCTGCGGAACTTGGGCTGGACTTTCAGAGATTCCTGACCTTGAACCGGACCTTGCTTGTGGCTGCCCG
Seq A exon
GTAAAATGGCCGAGGCACCGTTTTGGGGCAGACATGCATGCTCCTGGGCAGACATGGGACCTGCATGGCCACTGCAGCATCTTGCAGGGGACACATGCAGGTGCACAAGCCATGGGACATGGACATGCTTGGACCCAGAGAACAAATGCCAAGGCGTGGAGTAAGGGGGAGGCTAGGGCGCAGGACTTTATGTGGCTTGGCCCTGAGCTGGTGAACATGGGTAAGGAGGGGCTAAGGAGCTCAGGCAGGGTGCCTCTGCTCAGCTCTGACCCCTCCTTACCTACCCTTCAG
Seq C2 exon
GGATCACGTTTTCTCCTTCGATCTTCAAGCCCAAGAAGAAGGGGAGGGGCTGGTGCCCAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021101:ENSRNOT00000028645:2
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=PU(11.1=35.9)
A:
NA
C2:
PF0140314=Sema=FE(16.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTCTCCGTCATCCTGGTTC
R:
AGCCCCTCCCCTTCTTCTTG
Band lengths:
164-455
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]