BtaINT0026328 @ 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
chr23:28503864-28505438:-
Coord C1 exon
chr23:28505163-28505438
Coord A exon
chr23:28504140-28505162
Coord C2 exon
chr23:28503864-28504139
Length
1023 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGA
5' ss Score
7.75
3' ss Seq
ATTTTCTGATTCCTCCTCAGACC
3' ss Score
9.23
Exon sequences
Seq C1 exon
GGTCTCACACCCTCCAGTGGATGTACGGCTGCGACGTGGAGCCGGACGGGCGTTTCCTCCGCGGGTACAGGCAGGACGCCTACGACGGCAGAGATTACATCGCCCTGAACCAGGACCTGCGCTCCTGGACCGCGGCGGACACGGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCAGGTGAGGCGGAGAGACGCAGGAACTACCTGGAGGGCCGGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGACACGCTGCTGCGCGCAG
Seq A exon
GTGCGAGGGGTGCGGTGCCTCCCTGATCTCCCCTCGGGCTGGAGCTGGCTTCCCACGAGGAGAGGAAAATGGGGTCCCTGTGGGAACAGCGCCCCAGGTTCTTGTCAGGAGAGGGAGGAAATCCGCCCGGGTTTTCATATTCTGTGCAAGACCAGTTGCCCCACTTGTCTGAAGGACAATTAAGGAATCCAGCGTCTTTGAGGAAGATGCAGGAAACAATCCCTGAAATAGCTGGTCAGCGGTGCCCTGTGACCCTGGCCACCATCTTGTGATCCATGACTTTCTCTCTCAAGGCCTGTTCTCACCCTGAGAGCATCTTAGGAGGCCTGACTCCAGCTTTTCTGAATCATTCAGCCTCCAGCGGAGTCAGGACCTTTAGTCTGTATTCTCCCCCTCACATTTTTAGAGCGCCTATCCTAGTCTCTCATTCTAGAAATTTCCAAGGACTAATATAGATCATCCGTGATCTCTGAGATGATGCTGTTGTGCTGCTTTTTTCAAAACCATGCTCCTGAATATTCTGTAGCTCAGAGGGTAAAAAAGTTGTTAATACATCTGGGGATCTGATGTATAGCCTGGTGACTATAGTTAGTCTTGTATTATATACTTTTAAATTGATCTTAATAATTCTCATCATCCCAGTCGAATAGATGCGCACATAAGGTAAGTTGATAAATATATTAATTATCTTCATAGTGTTTCATATATTGTGAGTTTTCTTGTCTCAGTGGGGTTTCAGTCTGAGGTAGACCTTTACCTGCCTGGTTACTGGAAAGTACCCTCCACACACATGGGGAGTCTGGAGCTGATGCTAACATTTTTCTTTTCTAAAGCACTTGTGAATTATGCTTCATATATCAAAGCAACATGTAGTACACTCTAAATGTGTACAATTTTTGTTAAGTATAAATCGGTAAAGCTGGGTAAAAAATCACTGTTCTGTTCCTTCTCAGGGTGGTCACATGATGCTGCTTCAGTGACCCATGGAGGTAACACAAACTGAATTTTCTGATTCCTCCTCAG
Seq C2 exon
ACCCTCCAAAGGCACATGTGACCCGACACCCCAGCTCTGACCGTGAGGTCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGAGGAGATCTCACTGACCTGGCAGCACAATGGAGAGGACCAGACCCAGGACATGGAGCTTGTGGAGACCAGGCCTTCAGGGGATGGAACCTTCCAGAAGTGGGCAGCCCTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACGTGCCGTGTGCAGCATGAGGGGCTTCGGGAGCCCCTCACCCTGAGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002069:ENSBTAT00000031167:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.075 A=NA C2=0.290
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=89.2)
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:
GACGGCAGAGATTACATCGCC
R:
TCTCCACAAGCTCCATGTCCT
Band lengths:
343-1366
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]