BtaINT0072363 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012451 | HLA-DMB
Description
Bos taurus major histocompatibility complex, class II, DM beta (BOLA-DMB), mRNA. [Source:RefSeq mRNA;Acc:NM_001040481]
Coordinates
chr23:7189575-7191969:-
Coord C1 exon
chr23:7191688-7191969
Coord A exon
chr23:7189860-7191687
Coord C2 exon
chr23:7189575-7189859
Length
1828 bp
Sequences
Splice sites
5' ss Seq
CACGTAAGG
5' ss Score
7.47
3' ss Seq
TGTTTTTTCCTCCTGTGCAGGCC
3' ss Score
11.13
Exon sequences
Seq C1 exon
GTGGTTTTGTGGCACACGTGGAAAGCACCTGTGTGTTGGACGATGATGGGGATCCGAAAGACTTCTCGTATTGCATCTCCTTCAACAAGGATTTGCTGACCTGCTGGGATCCCCTGCAGGCCAGTATGATTCCTCGTGAATTTGGGGTGCTGAACGGCTTGGCCCGGTACCTCTCACAGTTCCTCAACAATAATAGTTACCTGATCCAGCGCTTGTCCAATGGTCTGCAGAACTGTGCCGCGCACACCCAGCCCTTCTGGAGCTCTCTGACCCACAGGACAC
Seq A exon
GTAAGGAGAGAGGGGTGCAGAGGGGCGGTGAGGAGAGGGGAGGCCTCGAAGGCTCCCTCTGTTGACAGGGGGGTTTGAGATGTGGGCAGAAAAGAAGCAGAAAAATGGGAGCACCTGTGATGTAGAAAGAGAGGGAAACAAGGGGGTTGACAGGGGTGGGGCTGGAATGCAAACCAGGTGGTGATATTTGAGCAGGCAAGGAGCTTCTGCAGGGAGAGTAAAAATGTTTTCCTTCGATTCAGGGCATCTCAGGAGACAGATCCAAGTTCAGCCAGGGGTTGAACTGTCAGAAGAACCAGAATGGCTTTCCCCAAAGGGCTTGTGCCTCTGTATCCCAGGTTCTGGTGTCCCGGGTCTAAGATGGGCCCAGGCATGGGACAATTTGGAAAGCCTCCCAGGGAATTCTGAAGCAAAGTGAAAGTGAAAGTAGCTCAGTCATGTCCGACTCTTCGAGACCCCATGGACTATACAGTCCGTGGAATTCTCCAGGCCAGAATACTGGAGTGGGTAGCCTTTCCCTTCTCCAGGGGATCTTCCCAATCCCAGGATCAAACTCAGGTCTCCCACGTTGCAGGCGGATTCTTTACCAGCTGAGCCACAAGGGAAGCAAACTCTCTCCCTAATCACTTGCATAGAGAATGACTTGAGATTGGCAAAAAAAAAAAACAACCCAAACTTGAAGTTCTCTATCTTAAAAAGTATTGTGTCTCAAGATATCATTTCTCAGAATTGCCTGGGAAGGTGCTTGTTAAAAACGCAAGTCCTGGGACTTCCCTGGTGGTCCAGTGGTTAAGAATCAGTGCTTCCGGTGCAGGGGGCACAGGTTCAATCCCTGGTCAGGGAACTAGGATCCTGAAAGCGGTGTGGCACAGCCAAAAACAAAAACAGAAATAAATTTAAAATAAAAACATAAAAATAAAAATGCAAGTCCTTGAGAGCTACTGCAGATCTGTTGAATAAAAATATCCAGGGATACAGGCTAGGGAATCTGCGTTTTAACACAGTATCTTGGATTTTTATTGAGGATTTTATTTGAAAGACACCCAAGCAAGCTGAAGGGTCACCTAGAAAAATAAATTACTAACAGACGGCAATATGAATGATCTGATGAATTAGGGTCCACCCTCATCCAAATTTAAGAGTTGGTCCTGAATTAGTCTTGCTTCCTTAAACTATTCAGGCTTGCCAGATGGCACAGTGGTAAAGAATCTGCCTGCCAATGCAGGAGACTCTTGAGATAGGGGTTCAATCCCTGGATCAGGAAGATCCCCTGGCGTAGGAAATGGCAATCCATTCCAGTCTTCTTGCCTGGGAAATCCCATGGACAGAGGAGACTGGCAGGCTACGGTCCACGAGCTCGCAAAGAGTCAGACACGACTGAGCACGCACACATGCCTTAAACTCTTCAAGGAAAAAATACTTTTTTTACTGAGTTAATCTGTTCAATGAGATTTGAGGACAAGGGTGTTTTCCTACTTTTGCTCACCCCCACCTCTAAGTCTGGATGACAATTTGCTTTTATGTACTTGCAATGAATACAATGCCTTCTGAAACAGCTTGCAGTTCAGCCCCAGCTTTTACTTACGGTGACCAAACAGGATTTTGGAGGAACAAGAAAGTAAGGAGCAGGGATGGAGTGGGAGACAGGAAAGAGTACAGAGGAATATATTCCAGCTTCTCATTTTCAGAGGGATGTGTGCAGGCCTGGGGTGAGGGCCGGCAGGGTAGGTGGGCAAAATCCAAGAAGCATTGAAGTAGGAGAGAAACCAGGTTGGAGGAAAAGCCAGGGTGGTGCCCTCCTTCGTGACTGTTTTTTCCTCCTGTGCAG
Seq C2 exon
GCCCACCGACCGTGCAGGTAGCCAAAACCACTCCTTTTAACACGAGGGAGTCTGTGATGCTGGCCTGCTATGTGTGGGGCTTCTATCCAGCGGACGTGGCCATCACGTGGAGGAGGAACGGGCAGGAGGTCCTCCCACACGGCAGGGCCTGGAGGATCATCCAGCCCAACGGAGACTGGACATACCAGACCGTCTCCCATCTGGCCACAACCCCCTCTTTTGGGGATACCTACACCTGTGTGGTCGAGCACATTGGGGCTCCTGAACTCATCCTTCAGGACTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012451:ENSBTAT00000016520:2
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=0.031
Domain overlap (PFAM):
C1:
PF0096914=MHC_II_beta=WD(100=84.2)
A:
NA
C2:
PF0765410=C1-set=WD(100=87.5)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGATCCAGCGCTTGTCCAAT
R:
GAGTTCAGGAGCCCCAATGTG
Band lengths:
351-2179
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]