BtaINT0079081 @ 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
chr23:28470409-28470973:-
Coord C1 exon
chr23:28470866-28470973
Coord A exon
chr23:28470442-28470865
Coord C2 exon
chr23:28470409-28470441
Length
424 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
ATTGTATTTTCTTCTAACAGGTG
3' ss Score
10.46
Exon sequences
Seq C1 exon
AACCTCCTCAGACCTCCTTCCTCACCATGGGCATCATTGTTGGTCTGGTTCTCCTTGTCACTGGAGCTGTGGTGGCTGGATTTGTGATCTGGATGAAGAAGCGCTCAG
Seq A exon
GTAGGGAAGGGAGGGAGGGATCTGAGTTTTCTTGTCTCACTGGGGGTTTCAAGCCAGGTAGAAGTTTACCTGCCTCGTTACTGGAAAGTACCCTTCACACACATGTGGAGTCTGGATCTGATGCTAACATTTTCCTTTTCTAAAGCACATGCGAAAATGAAAGTGAAATTTTGACCTTCTTAATTCCAGTTGGGAACCAGGTTTCCAGCACTTGAAGGTCAGAAGGGAGGTCCTTGCTGAGGACAGACCACCACGAGGCAGTTGGTCCAGTCCTTACACGTCTCCCTTCTCTGTGTTCCTGATCCTAGCATGAGTTTTGGCCACAGTTCCAGAAAGTTCTCTGGGGTCCAGGACTAGGGGTTCCTCTAGCATCACATGATTCAGTCTTCTCTCTGGCTTCTCACATTGTATTTTCTTCTAACAG
Seq C2 exon
GTGAAAAAGGAGGCAATTATATCCAGGCTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020116:ENSBTAT00000011795:5
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=0.583
Domain overlap (PFAM):
C1:
PF066236=MHC_I_C=PU(6.9=5.4)
A:
NA
C2:
PF066236=MHC_I_C=FE(37.9=100)
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]