DreINT0018771 @ danRer10
Intron Retention
Gene
ENSDARG00000076104 | SEMA4B (2 of 2)
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B [Source:HGNC Symbol;Acc:HGNC:10730]
Coordinates
chr7:29983490-29983819:+
Coord C1 exon
chr7:29983490-29983601
Coord A exon
chr7:29983602-29983702
Coord C2 exon
chr7:29983703-29983819
Length
101 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
TGAGTGTTTGTGTGTTGTAGATG
3' ss Score
9.05
Exon sequences
Seq C1 exon
AACATTTCAAGTTTTTCTCTGGAAGCAGATGAAAAGGGTGAACCTATTATGGAGGACGGCCGTGGACGCTGTCCATTTAATCCAGAATACAGATCTACAGCTATTACAGTGG
Seq A exon
GTAAGTATACTCATGCAAAAAAGGCTATCGTTTTGTTTGAACTAAGCATCAAGGTTGATAAAGAGGTTGAATTAGGGATGATGAGTGTTTGTGTGTTGTAG
Seq C2 exon
ATGGGGAACTGTACACTGCTACTGTCAGTAACTTCCAAGGAAATGAACCCAGCATATATAGGAGTCTGGGCTCTGGCACTCCTCTGAAAACGGAGAACTCTCTCAACTGGCTCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076104:ENSDART00000109243:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.125 A=NA C2=0.025
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(5.1=54.5)
A:
NA
C2:
PF0140314=Sema=FE(9.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATTTCAAGTTTTTCTCTGGAAGCA
R:
CCTGGAGCCAGTTGAGAGAGT
Band lengths:
228-329
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]