DreINT0132765 @ 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
chr12:33736031-33736519:-
Coord C1 exon
chr12:33736381-33736519
Coord A exon
chr12:33736254-33736380
Coord C2 exon
chr12:33736031-33736253
Length
127 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGA
5' ss Score
8.51
3' ss Seq
GTGGCCTTGTTTCTTTTCAGTGT
3' ss Score
9.53
Exon sequences
Seq C1 exon
GAGAAACGTTAAGATGTCTGCAGTGTGTCGGTATTCCCTCAAAGACATCCAGACAGCTTTTAATGGGCCATTCATGGAACTTCAGGACTCCAAATGGAGGGAATACACTGGGAAAGTTCCGGATCCACGACCTGGTTCG
Seq A exon
GTGAGATGCTCTAAATCAAAACAGTCCCATAAACTGTCCCCTTTAAAACCTTGCATTGAAGTGTAGCATGGTTTCTATTTACACTCTCTGGGGAATGTTATGTAATGGTGGCCTTGTTTCTTTTCAG
Seq C2 exon
TGTATAACTGATGAGCATCGTGGCAAGCTCATAAATTCCTCTCGGGATCTGCCTGACAACACTCTGAATTTTGTTCGGAGACACCCTTTAATGTCCACCCAGATCCAGCCGGTGGAAGGACGTCCACTTTTGCTCCAGAAAGCTGCAGATTACACTAAAATCATTGTTCAACAGGTTGAGGGTTTGGACGGACGGACCTATGACATGCTCTTCATTGGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000088143:ENSDART00000131181:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.128 A=NA C2=0.053
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(11.7=100)
A:
NA
C2:
PF0140314=Sema=FE(18.9=100)
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:
CTGCAGTGTGTCGGTATTCCC
R:
GCAAAAGTGGACGTCCTTCCA
Band lengths:
255-382
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]