BtaINT0026330 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005182 | BOLA
Description
Bos taurus major histocompatibility complex, class I, A (BOLA-A), mRNA. [Source:RefSeq mRNA;Acc:NM_001040554]
Coordinates
chr23:27647069-27647739:+
Coord C1 exon
chr23:27647069-27647174
Coord A exon
chr23:27647175-27647469
Coord C2 exon
chr23:27647470-27647739
Length
295 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TTACCCCTCCCCGCCCCCAGGGT
3' ss Score
11.23
Exon sequences
Seq C1 exon
GCTGGACTCTCTTCTTCCCAGACCCCCGGGATGCGGGTCGTGGGGCAGAGAACTCTCCTCCTGCTGCTGCTGCTGGATGCGCTGATCCTCACTGAGACCAGGGCGG
Seq A exon
GTGAGTCAGGAACGGCCTCTGCGGGGAGGGGCGAGGGGACTGCCCGGGGGTCGGGGGGGCAGGACCCCCAGGGAAGGACCCCTCTGCCCCCGACTAGACCCGCCCCCTCCGCCTGGTCCCGTCCTGTCTCTCCCTTGCTTCCCGCCCCCTCCTCTCGCCCCCCAAGGCCTGGTCCTTCTCCGACCATTTCCGTATCACAAGCTTCTCTCCCCCTCCCCCGCTCCATGCCCGGTCACCTAGGACCCGGGACCCGCGTCAGGAGGAGGGTCCACATCTTACCCCTCCCCGCCCCCAG
Seq C2 exon
GGTCCCACTCCCTGAGGTATTTCTACACCGCCGTGTCCCGGCCCGGCCTCGGGGAGCCCCGCTTCATCTCCGTCGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCCCGGATCCGAGGATAGAGCCTACAGCGCGGTGGGTGGAGCAGGAGGGGCCCGAGTACTGGCATCAGGAGACGCAGAGAACTAAGGACACCGCACAATTTTTCCGAGTGTACCTGAACACCCTGCGCGGCTACTACAACCAGAGCGAGGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005182:ENSBTAT00000031166:1
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=0.165
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
Mouse
(mm10)
No conservation detected
Rat
(rn6)
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:
GAGAACTCTCCTCCTGCTGCT
R:
GGGTGTTCAGGTACACTCGGA
Band lengths:
299-594
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]