BtaINT0105600 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004547 | OLR1
Description
Bos taurus oxidized low density lipoprotein (lectin-like) receptor 1 (OLR1), mRNA. [Source:RefSeq mRNA;Acc:NM_174132]
Coordinates
chr5:100246248-100248096:+
Coord C1 exon
chr5:100246248-100246343
Coord A exon
chr5:100246344-100247850
Coord C2 exon
chr5:100247851-100248096
Length
1507 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
TAAATTTATTTCTAATTTAGTAT
3' ss Score
5.55
Exon sequences
Seq C1 exon
GTTTTGTTTCCTCTTGGAGGTGGTACCCTGCTGCTGTGACTCTAGGGGTCCTTTGTCTGGGATTACTGGTGACTGTTATATTGTTGATACTGCAAT
Seq A exon
GTAAGTGCTGAAGCAGGAAAGAAGGGAGAAAAAAAAATGAGGGCTTATAAACAGGGTTTATTAGTTGGTTTCATAGTAACTATAAGCCACCTTGATTTAGATACATTTGAGGCAGACTGTTTTTAGGAGTGAATGGGAAGATGAATGAGTTTATTGTGTTCTTCCCTCAAATAGATTGAGGCATGGATGAAGATTACGGATATTAGGTTTTTGTTTGATTTTGTTTCCGGAACTTCATGGATAGAGTCCATTTAAATCCCAGAATAATGAGGAAGGAAATAATTTGAAGTTACTAACCCATAAGACCACCGGAGGGACCCATAAAAAGACACTTCATTTAGTTCACATTGAGTTTTAATACAAATGATTAAATACCAATTTAAAGTTAACTCAGAAACACAGTCTTCATAAATACAATATTTAAAATAAAACAGTCTTTGGATTTACAATATGGCCATTTAGGAAAGAGGGGATGTCAAAGGAAAAGAAATGAAAAGGTGAAAGTGACCAAGAAGGGAAAAAAATGGCGATGATCATACATCTAATCCACCTATATATTTAGGTTATAGCTTTGAGCTATTTTGGCTCTCTAGAATCCTAGAATCCAATTTATGAACGCCTTTGAAGTGCTAATTTGTTCCTCAATGGTGTTTAAGGTCAAAAATCACTTATTTTTTCAATCTATAAACACTTTGTACCTATAAATCCTTTCCTAATGATGTGGGAGAAGAGCCCTTGACTCAGTGGTGGTCATTGGAAGAGTCTTCCTTTGAGGTTCTGATCACTTTTTAACAGGGTCAAGTATGGGTTTCAAGCCAAAGGGTCTACTTCGTACTGAACCATAAAACTTATAGAATCGAGACACTGGACCCTTAACATTTGTTGCCTGCTTGATTTCACAACCTTCCTTTCATCTCCACTCTTTCTAAAGACAAAAAAAAAAAAAAAAACAAGCTAAAATTGAAAAATTGTTTTCATATTCTTGCGAAAGCAGCTTAAAATAGTCCCATGGGAGAGTTTCTCAAAAACAGGGTGAGTGTCACAGTTTTTATGTAAAATCAGGAAGTGTGGAAGGTGGGGAGAGGGCAATTAAGACACAGAATTAATACACAGTAGAGTAAATCATTAATGACAAGTGCTACTAATAGTCACTGAGTATGATTGGTGTCTGCCTATTTTATATTATCTACATTTTACTTATGCCACTGATGAATGATTTAACTTGTGATTTCTTTTAACTTGTGTGTAACTCTCAGTAACAAGTAAATTCCTGTTTGTTTGTTTTTTATCACAAGTATCTGAGACATTTTTCAACATTAATATATATATATATGTATGTATATTGCAGAAATATAAAATAACTTCCAAATCCATAATTTGAGTAAAGTTGGGTTGATTTGTTGTCAAAACAGATGGCTTGATTCTGCTCTTTGATTTCTTCAAAATCCAGTGGAGGAATTTTTTTATTGGGAATTGGAATTGGAATCTAAATTTATTTCTAATTTAG
Seq C2 exon
TATCCCAGGTCTCTGATCTCATAAAGAAACAGCAAGCAAATATTACTCACCAGGAAGATATCCTGGAGGGACAGATTTTAGCCCAGCGCCGATCAGAAAAATCTGCCCAGGAGTCACAGAAGGAACTCAAAGAAATGATAGAAACCCTTGCCCACAAGCTGGATGAGAAATCCAAGAAACTAATGGAACTTCACCGCCAGAACCTGAATCTCCAAGAAGTTCTGAAAGAGGCAGCAAACTATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004547:ENSBTAT00000005975:2
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=0.084
Domain overlap (PFAM):
C1:
PF083915=Ly49=PU(22.0=84.8),PF041569=IncA=PU(16.1=78.8),PF0055814=Vpu=PU(26.1=72.7),PF145841=DUF4446=PU(24.5=69.7),PF148511=FAM176=PU(21.6=66.7)
A:
NA
C2:
PF083915=Ly49=FE(64.6=100),PF041569=IncA=FE(50.9=100),PF0055814=Vpu=PD(72.8=80.7),PF145841=DUF4446=PD(74.5=84.3),PF148511=FAM176=PD(77.5=95.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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:
CCTCTTGGAGGTGGTACCCTG
R:
AGTTTGCTGCCTCTTTCAGAACT
Band lengths:
327-1834
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]