BtaINT0130787 @ bosTau6
Intron Retention
Gene
ENSBTAG00000046924 | SEMA3G
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G [Source:HGNC Symbol;Acc:HGNC:30400]
Coordinates
chr22:49002412-49002744:+
Coord C1 exon
chr22:49002412-49002502
Coord A exon
chr22:49002503-49002627
Coord C2 exon
chr22:49002628-49002744
Length
125 bp
Sequences
Splice sites
5' ss Seq
TAGGTGGGT
5' ss Score
5.56
3' ss Seq
TGCCCCCACCCCAACCCTAGGAG
3' ss Score
7.98
Exon sequences
Seq C1 exon
CATGTGCTCCATCTGGAGCCCCGAAGCATGGAAAGTGGGAGGGGGAGATGCCCACACGAGCCCAGTCGTCCCTTCGCCAGCACCTTTGTAG
Seq A exon
GTGGGTGACACCCAGGCCAGGGCCGGCATGACAAAGGTGGGGGTTGGCCAGCATCATTGGGAAGGGATGGGCCAGGTTCAGGGCCTGGCCCTCCTCCCCTGACTCTGCCCCCACCCCAACCCTAG
Seq C2 exon
GAGGGGAGCTGTACACAGGCCTCAATGCCGACTTCCTGGGGCATGAGGCCATGATCTTCCGGTCTGGGGGTCCCCGACCAGCCTTGCGTTCTGACTCTGACCAGAACCTCCTGCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000046924:ENSBTAT00000065486:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.645 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(6.7=100)
A:
NA
C2:
PF0140314=Sema=FE(8.7=100)
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:
TCCATCTGGAGCCCCGAAG
R:
TGCAGGAGGTTCTGGTCAGAG
Band lengths:
199-324
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]