DreINT0018762 @ 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
chr7:29987884-29988327:+
Coord C1 exon
chr7:29987884-29988034
Coord A exon
chr7:29988035-29988116
Coord C2 exon
chr7:29988117-29988327
Length
82 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
TGTTTTTTTTTCTTTTGTAGTGT
3' ss Score
10.58
Exon sequences
Seq C1 exon
GAGTAAAGGTCTTGCTGGCAGTTCCGCAGTGTGTGTGTTCAGCATGGATCAGGTGGATCGAGCCTTTACTGGCCGTTACAAAGAGGTGAATCGAGAGACACAACAATGGTACACATACACTCAATCTGTACCTGAACCACGACCAGGAATG
Seq A exon
GTAAGACAACACACTCCCACATTTACACTCTACCTGTTCTGTACAAGTGGAGAGTCTCTTAGTGTTTTTTTTTCTTTTGTAG
Seq C2 exon
TGTATTACTAATGCCTCAAGGCAGCTGGGAATAGACTCCTCTTTGGATATGCCAGATAAGGTACTAAACTTTGTGAAGGACCACTTCCTGATGGACCGTCCTGTCAGAAGTCAGCCTGTGCTCTTCACACACACTGTGCACTACACACAAATCGCTGTGCACCACGTGAAGGGTCTCCACAGAGCTTATGACGTGATGTTCATTGGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076104:ENSDART00000109243:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.059 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(11.5=100)
A:
NA
C2:
PF0140314=Sema=FE(16.1=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:
AAAGGTCTTGCTGGCAGTTCC
R:
CTATTCCCAGCTGCCTTGAGG
Band lengths:
181-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]