DreINT0132613 @ danRer10
Intron Retention
Gene
ENSDARG00000011163 | sema3fa
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Fa [Source:ZFIN;Acc:ZDB-GENE-050513-1]
Coordinates
chr6:42914215-42914524:+
Coord C1 exon
chr6:42914215-42914282
Coord A exon
chr6:42914283-42914390
Coord C2 exon
chr6:42914391-42914524
Length
108 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAAG
5' ss Score
1.69
3' ss Seq
TTTGTTTTCATTCCCATCAGCCA
3' ss Score
6.47
Exon sequences
Seq C1 exon
GCGGAGTCGAAGGCAAGACGTGAAGTATGGAAACCCTATAAGGCAATGCAGAGGCTACAACTCGAATG
Seq A exon
GTGAAGAACAAATTTAATATACATCAATACGAAGGAGTAAAAGTTCTTTAGAAGTTGTTGTGATTTTGGCTATTGTTTTAGATATTATTTTGTTTTCATTCCCATCAG
Seq C2 exon
CCAATAAGAACACATTGGAGACAGTGCAGTATGGAGTAGAGGGAAGCACAGCCTTTTTGGAGTGTCAGGCCAGATCTCCTCATGTGTCCATCAAGTGGCATTTCCAGAAGGAGAACAGCGACCGGAGAAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011163:ENSDART00000046498:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=NA C2=0.111
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(35.7=83.3),PF0768612=V-set=PU(0.1=0.0)
A:
NA
C2:
PF0768612=V-set=PU(47.8=97.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGGAGTCGAAGGCAAGAC
R:
CTCTCTTCTCCGGTCGCTGTT
Band lengths:
202-310
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]