DreINT0132758 @ danRer10
Intron Retention
Gene
ENSDARG00000088143 | sema4gb
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Gb [Source:ZFIN;Acc:ZDB-GENE-111117-1]
Coordinates
chr12:33731906-33732311:-
Coord C1 exon
chr12:33732250-33732311
Coord A exon
chr12:33732172-33732249
Coord C2 exon
chr12:33731906-33732171
Length
78 bp
Sequences
Splice sites
5' ss Seq
ATGGTGTGT
5' ss Score
4.84
3' ss Seq
TGTTTCCTACATTTCACCAGGTT
3' ss Score
8.13
Exon sequences
Seq C1 exon
GTCCAGTCTCGTCCAGGACATCCAGATGGGAAGACGAGGCTGTTCTAATATCACAAGTGATG
Seq A exon
GTGTGTTTGCAAGCAAAAAAAACTAATTTTCTGAGCACTTTTATAAGCGGTATAATAATGTTTCCTACATTTCACCAG
Seq C2 exon
GTTTCGTCATGCACCGAACACGTGCGGTGATGGCAGGAGATGATGTGCTGCTACAATGCGAGATTCGATCAAACCTGGCCACCCCTCAATGGACGCTGAACAGTCAAGAACTGAAGGGTTATGGCGTAGATTCTGGCTACCGCACTGGCACAGACGGCCTCCTTATTATCGGTGCACAGAACCAACAAAGCGGACACTACCGATGTTATGCAGTGGAAAATAGCGTCTGGGTTCCTATTCGCAGTTACATTGTGAGAGTGCAACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000088143:ENSDART00000131181:11
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=0.240
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(30.0=68.2)
A:
NA
C2:
PF138951=Ig_2=WD(100=97.8)
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:
ATGGGAAGACGAGGCTGTTCT
R:
GTGCGGTAGCCAGAATCTACG
Band lengths:
182-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]