BtaINT0001474 @ bosTau6
Intron Retention
Description
Bos taurus major histocompatibility complex, class I, A-like (LOC616942), mRNA. [Source:RefSeq mRNA;Acc:NM_001206459]
Coordinates
chr23:27842253-27842933:+
Coord C1 exon
chr23:27842253-27842374
Coord A exon
chr23:27842375-27842663
Coord C2 exon
chr23:27842664-27842933
Length
289 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TCACCCCTCCCCGCCCCCAGGCT
3' ss Score
10.23
Exon sequences
Seq C1 exon
ACAAAGTGTTCATCCACCCGCTGAACTCGCTTCTCCCCAGACCCCGGAAATGCGGGTCATGGGGTCGAGAACCCTCGTCCTGCTGCTGCCGGGTGCGCTGGTCCTGACCGAGACCTGGGCGG
Seq A exon
GTGAGTGCGGGGTCTGGAGGGAACGGGCTCTGCGGGGAGGTGGGTGGGCAGGACCTCCAGGGAAGGAGCAAGCCCGCCGCCCTCGCCCAGATCTGCCCCCTCCCCCTGTCCCGTCCTGTCTCTCCCTTGCTTCCCGCCCCCTCTTCTCTGCCCCCCAAGTCCTGGTCCTTCTCCGACCTTTTCCGTCTCAGGAGCCCGTGGCCCTTCCCTCCTCCCAGTTCCGTCACCTCAGGCCCGGGACCCGAACCAGGAGGATGTCGGGCCGGGTCTCACCCCTCCCCGCCCCCAG
Seq C2 exon
GCTCCCACTCCCTGAGGTATTTCTACACCGCCGTGTCCCGACCCGGCCTCGAGGAGCCCCGCTTTATCATCGTCGGCTACGTGGACGACATGCAGTTCGTGCGGTTCGACAGCGACGCCCCGGATCCGAGGATGGAGCCGCGGGCACGGTGGGTGGAGCAGGAGCGGCCGGAGTATTGGGATCAGGCGACGCAGAGAACTAAGGACACCAAACAGACTTTCCGAGCGAACCTGAACAACCTGCGCGGCTACTACAACCAGAGCGAGGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007075:ENSBTAT00000009299:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.253
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(50.6=98.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
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:
CTGAACTCGCTTCTCCCCAGA
R:
GTCCTTAGTTCTCTGCGTCGC
Band lengths:
308-597
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]