DreINT0132767 @ 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
chr12:33733775-33734148:-
Coord C1 exon
chr12:33734033-33734148
Coord A exon
chr12:33733930-33734032
Coord C2 exon
chr12:33733775-33733929
Length
103 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAC
5' ss Score
7.29
3' ss Seq
TTGTGTATTTTGTGATACAGAAC
3' ss Score
6.64
Exon sequences
Seq C1 exon
ATGAGGGCTGGTTACAAAGAGCTGTGAAGATTATAGACCGTGTGCACATCATTGAGGAGCTTCAGCTGTTCCAAGAGAAACAGCCCATCATTAACATGGTGATATCACAAAAACAG
Seq A exon
GTACACCACTGATATTCAAAAGCAGCATGAAATCCTGATATAGGGACAAACACTTAATGGATAGATCCCCAAAAGGTCTTAGGTTGTGTATTTTGTGATACAG
Seq C2 exon
AACAGTATCTATGTGAGCGGCGCTTCTGGACTGGTGCAGGTTCCTCTGTCATCTTGTGAACGCTACACCTCCTGTTACGACTGTGTGTTCGCACGCGATCCGCTCTGTGGCTGGGATGGAAGAATGTGTGCTGAGATAGCATCTTATGCTAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000088143:ENSDART00000131181:9
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(12.5=100)
A:
NA
C2:
PF0143720=PSI=PU(68.0=65.4)
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:
AGGGCTGGTTACAAAGAGCTG
R:
ACACATTCTTCCATCCCAGCC
Band lengths:
242-345
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]