BtaINT0007564 @ bosTau6
Intron Retention
Description
Bos taurus major histocompatibility complex, class I (LOC512672), mRNA. [Source:RefSeq mRNA;Acc:NM_001076841]
Coordinates
chr23:28305794-28306281:+
Coord C1 exon
chr23:28305794-28306069
Coord A exon
chr23:28306070-28306185
Coord C2 exon
chr23:28306186-28306281
Length
116 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
CCCTTTCCTTTCTTCCACAGAAC
3' ss Score
13.15
Exon sequences
Seq C1 exon
AGCCTCCCAAAACACACATGACTCATCACCGCATCTCTGACCGTGAGGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGAAGATCTCACTGACCTGGCAGCGCAATGGGGAGGACCAGACCCAGGACATGGAGCTTGTGGAGACCAGACCTTCAGGAGACGGAACCTTCCAGAAGTGGGCGGCCCTGGTGGTGCCTTCTGGAGAGGAGCAGAAATACACGTGCCGTGTGCAGCATGAGGGGCTTCAGGAGCCCCTCACCCTGAGATGGG
Seq A exon
GTAAGGAGAGGGATGGATGGTCAACCTTATTATCAGGTAATCAGGAGCCTTCAGGAGAACTTCAGCAAGGTTAGGATTCATGCCTGAGGTCAGGGCCCCTTTCCTTTCTTCCACAG
Seq C2 exon
AACCTCTGAAGACCTCCGTCCCCATCACAGGCATCATTGTTGTCCTGGTTCTCCTCGTGGTCACTAGAGCTGTGATCTGGATAAAGAAGCTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038619:ENSBTAT00000052679:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0765410=C1-set=WD(100=91.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
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:
ACCCTGCGAAGATCTCACTGA
R:
ACGAGGAGAACCAGGACAACA
Band lengths:
256-372
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]