BtaINT0087838 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020674 | LTB
Description
lymphotoxin beta (TNF superfamily, member 3) [Source:HGNC Symbol;Acc:HGNC:6711]
Coordinates
chr23:27530436-27530755:+
Coord C1 exon
chr23:27530436-27530487
Coord A exon
chr23:27530488-27530683
Coord C2 exon
chr23:27530684-27530755
Length
196 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
ACTCTTCCTACCTCTTCCAGAGT
3' ss Score
9.14
Exon sequences
Seq C1 exon
GTAACAGGGACGGCTGACCCAGGCACCCAGGCACCTGCCCATCAGCGATTTG
Seq A exon
GTAAGAGCCCACCATTTTACCCTCCCTTCCCTGGCTCTGCCCCTCAGGGACTCCCAGCTCCCAACCATCTGCATCCCCAGATACTCTCTTCCTTCAGGAATCCAGATGCCCCATCCCTGGGCCCTAGCACCTTGTCCTCTGGGGGTGACCAGAGGACACCCTGTCCCCAACCGTGGACTCTTCCTACCTCTTCCAG
Seq C2 exon
AGTCCGGGGAGCTGCCCGAGGAGGACTCAGAAACTGATCTCAGCCCTAGGCTCCCAGCTGCCCATCTCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020674:ENSBTAT00000027554:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.640
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTAACAGGGACGGCTGACC
R:
CAATGAGATGGGCAGCTGGG
Band lengths:
124-320
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]