DreINT0132718 @ danRer10
Intron Retention
Gene
ENSDARG00000079611 | sema4c
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:ZFIN;Acc:ZDB-GENE-080303-16]
Coordinates
chr5:14033128-14033570:-
Coord C1 exon
chr5:14033413-14033570
Coord A exon
chr5:14033224-14033412
Coord C2 exon
chr5:14033128-14033223
Length
189 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAAT
5' ss Score
6.15
3' ss Seq
ATTTGTGCTCCCCCCTACAGCTC
3' ss Score
11.52
Exon sequences
Seq C1 exon
AAGTATTTGTACATTGGCTCCAGGTCTGAAGTTCTTCAGCTGCCCTTGGCAAACTGCAGCCGGTACCATTCACAGCCAGACTGCCTGCTGTCCAGAGACCCGTACTGTGCCTGGGACAGCGAGGGACGAGCTTGTGTCCGCATCGACCTCCATCGCGG
Seq A exon
GTAAATTCATCCATCTTTTCCGTGGTTCCATTCATGCTCTCCTCTTTTCGTTTTCCTCCTTTCGCATGGGCTTTCCACCCCCTCTGCTCTCCTCCACAGGTCCCTCTTTGTACTTTTAAGCTACATCCCCATAGCAGTGTGTCTAACAGCCTTCTGACACATCGTCAATATTTGTGCTCCCCCCTACAG
Seq C2 exon
CTCCACATCCACACTCTCGCAGGACCTCATGCTGGAGAGGTTCAACCGAGGAAAAGCCAAGTTTGATAAGCCTTTCTCCATCCCCAGTCCTGGTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079611:ENSDART00000160511:11
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:
PF0150811=Paramecium_SA=WD(100=69.8),PF0143720=PSI=PU(71.4=66.0)
A:
NA
C2:
PF0143720=PSI=PD(26.5=39.4),PF138951=Ig_2=PU(9.4=27.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTACATTGGCTCCAGGTCTGA
R:
AGGACTGGGGATGGAGAAAGG
Band lengths:
242-431
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]