BtaINT0026350 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047707 | BOLA-DOB
Description
Bos taurus major histocompatibility complex, class II, DO beta (BOLA-DOB), mRNA. [Source:RefSeq mRNA;Acc:NM_001013600]
Coordinates
chr23:7055642-7056638:-
Coord C1 exon
chr23:7056369-7056638
Coord A exon
chr23:7055924-7056368
Coord C2 exon
chr23:7055642-7055923
Length
445 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
TTTTTTCTCTCCCCTCCTAGTAC
3' ss Score
9.88
Exon sequences
Seq C1 exon
AAGATTTTGTGACCCAGGCAAAGGCTGACTGTTACTTCACCAATGGGACAGAAAAGGTGCGGTTTGTGGTCAGATTCATCTTCAACCTGGAGGAGTATGCACGTTTCGACAGCGACTTGGGGATGTTTGTGGCCTTGACGGAGCTGGGGAAGCCGGACGCCGAGCGGTGGAACAACCGGCCGGATATACTGGCCAGGAGTAGAGCCTCTGTGGACATGCTCTGCAGACGCAACTACTATCTGGGTGCACCCTTCACCGTGGGGAGGAGAG
Seq A exon
GTGAGGTGGGAGTTGGGGTCTCCTTGGTGGGAGCCTGGGCGTGGCTCTTCTTCCTTGTCCTGGGCAGTTTCCTGCTTCAGGATATCTATCCATCAGGGTCAGGTGCAGGGGAGACTATATATGACCTGTCCCCAGTTGTGACTCTGTCCTCAGGGGTCAGGTCGCTGTGGTCTTGGTCCCAGATACCAGTTCTCGGCGCCTTTGAGGGCTAGTGTCTTCCTGAACACAAGGAAAATTGTGGGTGTGTCTGATAAAGCCCACATCCTCCTTGCGGACACTGACACTTTCAGTGTCTGAGTCCTGGGGGTGAGCTTTCCCCACATTTCCGGTTGCCACGTGGGTGATCTGGGGAAGAGATTCAGGGCAGAGACAGCCCCTAAAGGCACTCCGGGGTTGGCTTTGTGGATTTCCTTCACCACCTCTCATTTTTTCTCTCCCCTCCTAG
Seq C2 exon
TACAACCAGAGGTGACGGTGTATCCGGAGAAGACCCCAGCCCTGCAGCACCGCAATCTGCTGCTTTGCTTGGTGACAGGTTTCTACCCAGGAGACATCAAGGTCACCTGGTTCCGGAATGGGCAGGAACAGAGAGAGGGGATCATGTCCACTGGTCTCATCAGGAATGGAGACTGGACCTTTCAGATGACGGTGATGCTGGCCATGACTCCTGAGCTTGGAGAGGTCTACACCTGCCTCGTTGACCATCCCAGCTTGCTGAGCCCTGTTTCTGTGGAGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047707:ENSBTAT00000065976:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0096914=MHC_II_beta=WD(100=82.4)
A:
NA
C2:
PF0765410=C1-set=PU(93.5=90.5)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTGTGGACATGCTCTGCAG
R:
CACTCCACAGAAACAGGGCTC
Band lengths:
345-790
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]