RnoINT0105313 @ rn6
Intron Retention
Gene
ENSRNOG00000056219 | Olr1
Description
oxidized low density lipoprotein receptor 1 [Source:RGD Symbol;Acc:620515]
Coordinates
chr4:163239849-163242953:-
Coord C1 exon
chr4:163242838-163242953
Coord A exon
chr4:163242563-163242837
Coord C2 exon
chr4:163239849-163242562
Length
275 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGT
5' ss Score
8.54
3' ss Seq
TTTTTTCTTTCTGCCTGCAGCTT
3' ss Score
11.48
Exon sequences
Seq C1 exon
AACTTCGTCTTACAAGCAACTTCCCATTCCACCTCCCCATTTTGGATGGGATTACATCGGAAAAATCCCAACCACCCATGGCTATGGGAGAACGGCTCTCCTTTGAGTTTTCAATT
Seq A exon
GTAAGTCTACTACTGCTCTTGGTGGTCATTTTGAGTGTTCTATTTCTGTCTGGACCTGTTTTGAAGTCCCTGTCACATTCCACCTATGTCCTCTTCTTGTCAGAATGAACAGTGGTAAATACACTAAAATCACAAGAGGGTTTGTCATTTGCCCCTTCCTACCTTGCTGGCATTTTCTTTCCCATTACTGCTGATTTCAAGCTTTGAGATGTGGTTGATTTCTAACATAAAGATAATATGTGTCCTGTTTTCTTGTTTTTTCTTTCTGCCTGCAG
Seq C2 exon
CTTTAGGACCAGGGGCGTTTCTTTACAGATGTACTCATCAGGCACCTGTGCATATATTCAAGGAGGAGTTGTGTTTGCTGAAAACTGCATTTTAACTGCATTCAGCATATGTCAGAAGAAGGCAAATTTATTGCTAACTCAGTGAAACTAAGGATTCTGGAGAAGAACAGGAGAAGACCTTTAACTGTTGTTTTGAAATTTAAGCTATCCTTTCTTGGGTGTAAAACATGTGGCCTTGACAGCTGTCAGTTACTTTCTAACTGCAGTTCACCTCAACAGAGACAAAGACCAGAAGCAAAAACCCGGGGGTCCAGCTGATGGCATCTTTGTATCAAAAGTTGTGAATTCAATTGTTTATCCATGTACACTGGCCCCGCCCCTCCCAAGACTCCCAACCAACCTGCAATCCTTTTTTTCTTTCTTGTTTTAAACTATGCCTCCTGTCTGACCTGGGGGATGCTTTCTGCTCAATTTCCTCTACCTCAGGTATGCCTTCTGTTGCTGCATGAAAGACAGAATGTAGAAAACCTTCTTCAAGTGCAGGCAGAGAGCTCAAAGTTAAAAACATGCCTAAGAAATAGCATGCAAAGAAACAGAACTGGAAAAGCTACACTGTACGCAGGAGCTCATGGTCTCTAAAAAGCTATGGCTTGATCTTCACGACTTGGGTCCATCTCCAGACTGCACCATTTACACATTTATGTTTTTTTATTTTATTTTTATTGTGTGTTTATGGATAGTTGGCCTATATGTATCTCTGTGTACCACATGAGTGTCTCCATTCAGAAGAGGGCATCAGATTCTCTGAAACTGGAACTGCAGATGGCTGTAAGCTACTACATAGATGTAAAGAATTGAATTCATGTCCTCTGAAAGAACAGTCAGTACTCTTAACCATGAACTATTTCTCCAGGTCCCGTGATCATTTCTTGTATCAGCTATTTCTTCACATTTGCTCTACCAAAGAACAGAGCTTAAAACAGTATTTTATAAAGCCATAGAATATGGCCCCAAAACAAAACTAGAATTTTTCCCTTAAATTGCATACTTTGTAGACAGTCTCTCCTTGACCCTGCCATGCCATGCTATGACTTAGAAACATACATGACCAAAATGGATGAAACTCAGTTGAAGAACAAGTTCTTAGAATCACCTGAGCTGGGTATAAAAATATTGTTCTATGGGAACAGATGGATTTAGAAATATCTATTATCAGGGCCTCCACCATCCCCACAAGTCACAGACTCTTCCATTTCAAAGGAAGCTTTCCATTATGCTAGAGGTAATATAGCATATATGTCATGTATATGAGTGTGTATTTGTGTGTGTGAGTGTGTGTGTTCATATGCTAGATACGTCCTTGAGAAGATGAGACATTGGCAGCTTTGTGTGTAATGAATTTGCAATAATCCAAATTTGTAAGTAGTTTCCATGGTTCCTTATAGTGATGACATCACCACAGCCAAGATGATGAGCATACCTGTTGTTTCTGCCCCTTTCCAATGCTTCCTCCCTAGAACAAACACCAATCTGTTGTCAGTTGTCATTTCATAGAGTTTATAATCTTGTTTTTAAGAGAGAATCTCATTATATAGTTCTGACTGCCCTGGGACTCACTACACAGACCAGCCTGGCCTCCACCTTCCAGAGTTCCTCCTGCCTTTGACTCACAAGTGCTAACACTGAAGGAGTGCACCGCCATGTATGGCTCATGCAGTTTATGTGAATGGAATAGTATAACACATCCAGATTTTCTCAGTTCAGTTTCTTCCACTTGGTGCTATTATTTTGGTATTCATACATCTCTGCCTCAGTGTTTGTATCAGTTCTTCAATTTTTTTAAAATGTTGATCATTCCCCTGGTGGGTACATATTGTCATTTTTATCTGTGTATTTGTTGATGTCATTTGGGTTGTTTTTGTTTGGGGTCACCTACAAATAAAGCTGCTATGAATGCCCATGGACGATTCTGGTTTCTCATGTAAGCACCTCTGAGTGTGACACTTGGGTCATTCAGTGTGTGAATATATGGTTGGCCATGTTAACCATTGCTTTTTGAAATTTTCAATTTTTTTTTAAAATTAGTCGACTTTACATCTCAACTCCAATTTCCTTCCCTCCTCTCCTCTCAATCTTCACCCACCTCCCTCTCCTACCCCCATCCACTCTTCCCTTTCTCTTCAGAAAAGAGGAGGCTTCCCACAGATGTCAACCAGCCTTAGCGTATCAAGTTGCAGTAAGAATAGGTTTATCATCTTCTATGAAAGCCTTAATTTTTAGACTTATCACTGTATATGCAGTATTTTGTTTGCATGTATGTATTGGTACCACATATATGCCTAATACCAGAGGAAGTCAGAAGAGGGCATGGTATCTTCTGAGACTGGAATTACAGACATTTTTGAGCCATCCTACAGACTCTGGAAATTGAACCCAGGATTTCTGGAAAGTTAGGCAGTGCTCTTAACCCCTGAACCATCTCTTCAGGCCCTATAGCAATCTTTATTGATATGTAACTGTGTATAATTGCACTTTTAGTTTGAAGTTCTTAAATGGCAAATAGTCTTGAATTTATTTTCATGTTATCATTTACTGTCTGTACATTTTCTGTAATGAAATAACTAAGCATATCTTTTGAGAATTTTATTTTCTTACATTTTAAATCTGAAGGATTTACATACATACTGGAGAATAAAAACAGCCTAATGTGTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056219:ENSRNOT00000086390:7
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:
PF0005916=Lectin_C=FE(36.2=100)
A:
NA
C2:
PF0005916=Lectin_C=PD(37.1=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:
CGGAAAAATCCCAACCACCCA
R:
AGCTGTCAAGGCCACATGTTT
Band lengths:
303-578
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]