BtaINT0105603 @ 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
chr5:100253735-100255640:+
Coord C1 exon
chr5:100253735-100253850
Coord A exon
chr5:100253851-100254455
Coord C2 exon
chr5:100254456-100255640
Length
605 bp
Sequences
Splice sites
5' ss Seq
CTTGTAAGT
5' ss Score
8
3' ss Seq
TTTTTTCTCCCTGCCTGCAGGTT
3' ss Score
12.87
Exon sequences
Seq C1 exon
GAATTCATCCAGCAAACAATTGCCCATTCCAGTTTCCCCTTCTGGATGGGGTTGTCAATGAGGAAACCCAATTACTCGTGGCTTTGGGAAGATGGTACTCCTTTGACGCCCCACTT
Seq A exon
GTAAGTTTGATGCTCTTTTTTAGTTTTGTTTATTTATTTATTTCTATCTTTGACTGCACCGGGTCTTTTTTGCTTTGTGTAGGCTTTCCCTAGTTGTCACGCGCATGGGCTGCTCCCTCATATGATGTGTGGGCTTCTCACTGCAGTGGCTTCTCTTATTGCCAGGCATGGGTTCTAGCGGATGGGCTTCAGTAGTTGTGGCTCTTGGGCTGTAGAGCACAGGCTCAGTAGCTGTGGCATATGGGCTTAGTTCCTCCAAGGCATATGGGATCTTGCCAGACCAGGGATCGAACACATGTCTCCTGCATTGGCAGGCAGATTCTTATCCACTGAACAACCAGGGAAGTCCGTAAGTTTCTTATTCTTCACTGAACCTACTAGTGAAGTTACTGCTGCATTCCATGCAGTGTCCTACTCTTGCTGGAAAAAAGCCTGGGGAATTTCTGAATCTCTCTCTCCAACTCTCTCACACAAGGACCTGCCCATTTACCCATTCAGATCTTCTCTTACCTTTTCCTGCTCACATTTATTAATGACTTGAAGCTTTAAGACAAGGTGGCAGTAAATCTAATTTTTCTGTTTTTTTTTTTTCTCCCTGCCTGCAG
Seq C2 exon
GTTTAGAATTCAGGGAGCTGTTTCCCGTATGTATCCTTCAGGGACCTGTGCATATATTCAAAGGGGAACTGTTTTTGCTGAAAACTGCATTTTAACTGCATTCAGTATATGTCAAAAGAAGGCGAATCTATTGAGAGCACAGTGAATTTGAAGGATCTGGAGGAAAAGAAGGAAACCTTTGAATTCTCTTCTGGAATTTAAGCTATACTTCATCACTTAGATGTAAACCATTAGAGCCCAGGGAAATGCCTGCTACTGGTTGAGTGCAGAACTCCTTAGCAGAGACTGGCCCAGCTGCCTGGCACCTTGATAGCAAAAGTTGCAATTCCCTCTGTATATTTTTCCCTAACTTGTTCCAAGTCCTCCCCTGCAGGACTTCAGAGAAGTCAATTTTTCTGTTTCCATTGTTTCTAAGAACTTGTTGCCTAACTCAAGGTCACAGCATTTTTCTCACTTTTGTCCTATGCTTTCTTCTAGGCATTGTAGAGTTTTAGATTTTACATGGAAATCTAGAACTTATTTTAGATTAATTTCTAAGTGATATATGGATGTATGGAAGTTTTCTGTTTGTTTTTTGCTTGTGAGTATTCAATTGTTTTTGCAACATTTGCTGAAAAGACTATTCTTCCTTCACTACATTGCCTTTGCACTGTTGTCAACAATTATCCATACATGCCTGGCTCTATTTCTGGATTTTCTATTCCTTTCCATTTATTTATTTATTATTCTTGGCTTACAACATCACCATGATATTTTGAATTCTATGGTTCTTTAATATATCTTGGAATCACATGGTAGTAGTTATTCATTGTTGTTCTTTTTTAGAGTTGTTTGGTTAATCTATGCTTTTGTATTTCTGTCTTAAATTGGCTTGTCCATTTCTAAAAAAACTTGAAATTTTGAATTGCACTGAATCCATACATAAATTTAGGGAAAATTGAATTCTTAAAAATACTGATTTGTTCAACTCATGAAAAAGGTGTATTGCTCTATTTAGGTATTCCTTATTTTCTTTAAGCAATGCTTTTTAATGTTCTTTGTGTAGATATTGTTAGATTATCATCATGTATTTCACATTATTTATGCTACTGTAGATAGTATTGTTATCATTTGTTGTTCTTATTTTCAAAGTCTTCTGCTAGTATGTAGAATTATAATAAAGTTTGATATTAATATTATACCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004547:ENSBTAT00000005975:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF041569=IncA=PD(3.1=12.8),PF0005916=Lectin_C=FE(35.8=100)
A:
NA
C2:
PF0005916=Lectin_C=PD(36.8=79.6)
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:
ATTGCCCATTCCAGTTTCCCC
R:
AGGCATTTCCCTGGGCTCTAA
Band lengths:
349-954
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]