BtaINT0105602 @ 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
chr5:100253275-100253850:+
Coord C1 exon
chr5:100253275-100253414
Coord A exon
chr5:100253415-100253734
Coord C2 exon
chr5:100253735-100253850
Length
320 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
AGAAATGTTACTCCCCACAGGAA
3' ss Score
7.27
Exon sequences
Seq C1 exon
GTCCTTGTCCCCAAGACTGGCTCTGGCATGAAGAAAACTGTTACCAATTTTCCTCTGGCTCTTTTAATTGGGAAAAAAGCCAGGAGAACTGCTTGTCTTTGGATGCCCACTTGCTGAAGATTAATAGCACAGATGAACTG
Seq A exon
GTGAGTGTTCAACAGATGTATGGGATGTGTGTCGGGCTGGAATATTGGGTCATAGGTAAGTAGATCTTGTTTAGACCCTCAGTAGAGGAGTGCTTGCTTAAGAATCAGAACATGTACATGATTTCTAGCCTTGTGTGGCCACTGGATATGTGCATGACCTTGGATGGACAGGTTACTAAGCATTTCTAGGCTCCACTAGACATCGCTGTAAAGCCATGGAGAAGATGTCAAAGTTCTTTTTGAGTTCTTTAGTTTTGTGACTCTAATCTAAAAAGTCCACATCCACTCATTCATCGACACAGAAATGTTACTCCCCACAG
Seq C2 exon
GAATTCATCCAGCAAACAATTGCCCATTCCAGTTTCCCCTTCTGGATGGGGTTGTCAATGAGGAAACCCAATTACTCGTGGCTTTGGGAAGATGGTACTCCTTTGACGCCCCACTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004547:ENSBTAT00000005975:4
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:
PF083915=Ly49=PD(12.6=34.0),PF041569=IncA=FE(28.6=100),PF0005916=Lectin_C=PU(25.5=57.4)
A:
NA
C2:
PF041569=IncA=PD(3.1=12.8),PF0005916=Lectin_C=FE(35.8=100)
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:
TTGTCCCCAAGACTGGCTCTG
R:
GGGCGTCAAAGGAGTACCATC
Band lengths:
247-567
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]