BtaINT0079082 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020116 | JSP.1
Description
Bos taurus MHC Class I JSP.1 (JSP.1), mRNA. [Source:RefSeq mRNA;Acc:NM_001040498]
Coordinates
chr23:28470223-28470441:-
Coord C1 exon
chr23:28470409-28470441
Coord A exon
chr23:28470271-28470408
Coord C2 exon
chr23:28470223-28470270
Length
138 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CTGATCTTATTCTCCCCCAGGGA
3' ss Score
10.89
Exon sequences
Seq C1 exon
GTGAAAAAGGAGGCAATTATATCCAGGCTTCAA
Seq A exon
GTAAGTATGGAGGGGGTGATTCCTGAGACCCTTGTGTGGGTGCAGACAGGAGGCCATGGGGGCTCACCCTCCTTAAAGTTCCTTCTCTAGTTTCTCTCCTATGGGTTCTGACCACATCCTGATCTTATTCTCCCCCAG
Seq C2 exon
GGAGTGACAGTGCCCAGGGCTCTGATGTGTCTCTCACGGTTCCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020116:ENSBTAT00000011795:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.583 A=NA C2=0.059
Domain overlap (PFAM):
C1:
PF066236=MHC_I_C=FE(37.9=100)
A:
NA
C2:
PF066236=MHC_I_C=PD(51.7=88.2)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]