DreINT0018764 @ 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
chr7:29988409-29989688:+
Coord C1 exon
chr7:29988409-29988524
Coord A exon
chr7:29988525-29989530
Coord C2 exon
chr7:29989531-29989688
Length
1006 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGT
5' ss Score
6.64
3' ss Seq
TCCCGTCTCTCCACAAACAGGGT
3' ss Score
9.18
Exon sequences
Seq C1 exon
CTGATGGGCGTCTGCAGAAGGCTGTAAATGTAGCTGGTATGATGCACATCATTGAGGAGATCCAGCTGTTCTCAGAACAACAACCAGTACAGCAAATAGAGCTGGATTCAGCTAAG
Seq A exon
GTGTGTTTGTGTTCTATATTATGTGGTTTACAAGGACACTAAATTGTATAGTGACATAGGTCTGACTGAAGTGTAATACTGATAAGGTGATTTTTCTTTACACTTAAAATCATACTTAACAGGGTGATATTCGCAGTTTAACAGGTTTTGATATTCAAATTTTTAAGGTTTACGGATAGAGGTAGGTTAAGTCCATATAATAAGCTATTTTTACAGTATAAAATACATTACACCTATGGAGAGTCCTCATAAACCACATGAATATATATTTATATGTTTGTGTGTCTTTATAAATTCAGTGTGTTATTTTATATATTTAATAATATATTCATGTTTTGGCAAAGCTTTTTAAAGTTTTTATTTTTTTATTTTTTTTTATTTATAAAGTTTTAAGTAAGTAACTGTTTTTTTGTTTTTTTAAATATGTGAATAAAATATAATAAACAACCCCACCCCCACACACCAACAGCTGTATACTGTGCTCTTCATATTAATCCAAACATTTGTCATGTCGATGTTAAATAAAGGTGGAGTAACAATGGTTGATGATACATATAAATGAAAACCGTAATGTCCAGAAATGATGCACAAATAAATGAATATATAAGTAAATAAATAACATGTGTATATATAGGTAATAAATAAAAAAATAACCAAAATATTTCATGACTGACAATACTGATGTCCAGTATTAAAGTCTATCAATGGTAATGAATTAAGAAAAGGGGCCCAAATATAATCAAAGTCTGTGGACTTTTGCATAAACATAATTTTCCCAGGGATACTATATAATACACACTCAATAATCAAGTGTTGAGCTCTGGGTGGTAAAATTAACATTTGAAATCTGACACATTTAATGTCACTCTCAGCATTGATTTGTTAATAATGACAAAAAAAATAATACAGTCCCTACATTTCTGAACGGTGTACTTGTATTTCAACTTCTGTTCTTCAAAGTGTGTATTTCACCCTCTCACTCTCTGTCCCGTCTCTCCACAAACAG
Seq C2 exon
GGTCTGTTATTTGTGTCGTCACACTCTGGCATTGTTCAGCTGCCAGTAGCAAACTGCAGTTTCCATAACAACTGTGGCGAGTGTGTTTTAGCCAGAGACCCATACTGTGCTTGGACAGGCACACACTGTACTGACGTCACACTTGTCCCACCACAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076104:ENSDART00000109243:12
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(8.8=100)
A:
NA
C2:
PF0143720=PSI=PU(68.6=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGATGGGCGTCTGCAGAAG
R:
TTGTGGTGGGACAAGTGTGAC
Band lengths:
272-1278
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]