RnoINT0086065 @ rn6
Intron Retention
Gene
ENSRNOG00000061373 | Loxl3
Description
lysyl oxidase-like 3 [Source:RGD Symbol;Acc:1311011]
Coordinates
chr4:113868675-113870791:+
Coord C1 exon
chr4:113868675-113869018
Coord A exon
chr4:113869019-113870627
Coord C2 exon
chr4:113870628-113870791
Length
1609 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GATCACCTCCCTCTCCATAGGCC
3' ss Score
11.09
Exon sequences
Seq C1 exon
TGCCCCCCCTCCTTGAGCCCTAACCGCCATGAGAGCTGTCAATGTGTGCTATTGCTGCCCGTGGCGACTACTGCTGCTGCACTTTCTGTGCAGCTCCAGTATGGGGTCTCCGTCTCCTTCTACCGACCCAGAGAAGAAGGTAGGAAGCCAGGGGCTGAGGTTCCGTCTGGCTGGCTTTCCTAGAAAGCCCTATGAGGGCCGTGTGGAGATACAGCGAGCCGGCGAATGGGGCACCATCTGTGATGATGACTTCACGCTGCAGGCTGCCCACGTCCTCTGCCGGGAGCTGGGCTTCACAGAAGCCACCGGTTGGACCCACAGTGCCAAATACGGCCCAGGAACAG
Seq A exon
GTGAGCAGTGCTCTGGGCTAGCCCAGACATTACCTCAGTGCAGCTCAAGTACAGTGAGAAGAACAGAGTACCATGGTGGCACAGCCAAAAGGACATAGGACACCAAGAATGGATAGAATTAAGCAAATCCACAGGCAATAAACCAACATACTAATTTCAGGGCCATGTGACCTGAGGCCAGCCAGTACTTTCCAGGAGCCTCCAGTGTTCCATGTGTACGGTGAGGAGGGGGTTAAGTTCTCCCCTGCAAAGTAAGATTCTGTAGAGCTATGCAGGGGATCCCTGAATGATCCAAGTGCAGTTGACTCAATGATAATAAGAAGGCAGGTGAATGGTATCTGTATGTCCCCTAGCTGGAAGGGGTCATACACTATAGCTGACAAAATCAGGATCCAAGCCAAAGCTAAAACCAGCAAGCAGGAACTCATGTGGAGCAAATCTGACAGATGTGAGGGTTGGAACAGAATCCTCTGAGGTTGAAAGTGCTCAGACCATATGGACCTACACTAGGATTGGTGGATGGACATGGGTACAACCTGCTGTTCATCCACCCTCCCCATTCCCAGTTGCTCTACTGTTTCTGAAATAAACGTCAGGAGGGAACACTTTGAGAGGGACAGTAGAAAGTGGAAATGCTCAGAAATCGAGTGCTTTCCCTGCACTCAGTCCTCCGGAGAGAAGAAGGGAATGAGGGAGGAAGGTGGAGACAGACAGACAGACAGAAAGGCAGAGAGGAAACCACTTTCAGAAAGCCACTTTCAAGGGGAATAGTTAAAGAAACCAAAAGTTTGGCACAGAAACAAACAAACAGAGCCTCACTTAGCAATTACACGATGGCTGGGTTCAACCCGGGAAGGACAGTCAGTCGTGGCTGAAGATTTTTCTGGGTGGCATCAAAGGACTGAATAAGACCTAGCATGGGAAAGTTGTAAAGACCCACAAGGACTTTCTGATAGTTGTGTGGCCTCCTAAGGCAGAAAGGTAAAACCCTGTTAGACTACGTGAGGTGCCCTGAACGCTGGATGGGACACGTACTTTTCTGGAGGTTCCTCCCAGCTTTGGGTGGTCAGTGACAGCCAGTATGGTCCAGAAAGTAAAAACAGGGTTTTTGTGGCAGTAGGCAACATAGGTATACAGGAAAACGCCACCGGGGAGGCGGCGGGGTGAAGTGAAAGAATCTAAGCTTCCCAAGTATCAGTGAGAGAGGTCAGACTCTTAGGCAAATTACATCATGTTTTGGAGCCCCAGTCTATATTTATATAAAGTAATCTTCTGGCAGCTCCAGCCTAAGAATGGTTGTATATATACTACAGCAAAGCATCTGGCACATAGTAGGTACTTAATGATAGCTGTTATTGAACGAATCCTTGTTGATATTAGTGAGAATTAAAATGTGGATTCTCTGTTATTGGTTTTATCTTACCCTAATCAATTCTTCAGTGTCCCAGATCACCACTAACCTTGCATCAACCTTACACCCTCTTTCCTCTTCCCCTCCGGAGTTCCCTGTCTCTTCCCCATCTTTTTCTCATCAAAGAGGATTAGCCTCAAGGCTGTGTGAGGCCACCATCACTCTGTCAACACTTCTCGATCACCTCCCTCTCCATAG
Seq C2 exon
GCCGAATCTGGTTGGACAATCTGAGCTGCAAGGGTACTGAAGGAAGTGTGACTGAATGTGCCTCCCGGGGCTGGGGAAACAGTGACTGTACCCATGACGAGGATGCTGGGGTCATCTGCAAGGACCAGCGCCTTCCCGGTTTCTCAGACTCCAACGTCATTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000061373:ENSRNOT00000081196:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(57.3=51.9)
A:
NA
C2:
PF0053013=SRCR=PD(41.7=72.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGTCTCCGTCTCCTTCTACC
R:
AGCATCCTCGTCATGGGTACA
Band lengths:
348-1957
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]