BtaINT0026329 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002069 | BOLA
Description
Bos taurus MHC class I heavy chain (BOLA), transcript variant 1, mRNA. [Source:RefSeq mRNA;Acc:NM_001038518]
Coordinates
chr23:28502524-28503043:-
Coord C1 exon
chr23:28502996-28503043
Coord A exon
chr23:28502831-28502995
Coord C2 exon
chr23:28502524-28502830
Length
165 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CTGATTCTTTTCTCTCACAGTTT
3' ss Score
9.97
Exon sequences
Seq C1 exon
GCAGTGACAGTGCCCAGGGCTCTGATGTATCTCTCACGGTTCCTAAAG
Seq A exon
GTGAGACCCTGGAGAGTCTAGATTGGAAGGAGCATTGGAGCAGAGGGGACACATTAGGCCTGGCGGGGATCTTTGAGTGGGACATGTGGGCATGTGGGGGGCTGTGAAAAATGTCAGCCCTTACATGACTGACCTGAACTGCTTCCTGATTCTTTTCTCTCACAG
Seq C2 exon
TTTGAGACAGCTGCCTTGTGGGGACTGAGTGATGCTGCATCCCGCTATGTGACTTCAGATCACCAGACACCTCTTTCTGCAGCTGCATCTGAATGTGTCTGTGCTCCTATTAGCATAACATGAGGAGTTGGGGAGACTGGTCACCCCTGCCCACCGCGCCCCTTCCCCACCCTGACCTGTGTTCTTCTCCCTGATCCACTGTCCTGTTCCAGCAGAGACGGGGCTGGGCCGTCTCCATCGCTGTCTTTGCTTCATATGCACTGAGTAATGATGTCTTATTTCCTCTTTGAAAATAAAATCTGTATAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002069:ENSBTAT00000031167:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.059 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF066236=MHC_I_C=PD(51.7=88.2)
A:
NA
C2:
NO
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
(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:
GCCCAGGGCTCTGATGTATCT
R:
ACAGGACAGTGGATCAGGGAG
Band lengths:
244-409
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]