RnoINT0086081 @ rn6
Intron Retention
Gene
ENSRNOG00000015727 | Loxl4
Description
lysyl oxidase-like 4 [Source:RGD Symbol;Acc:1308588]
Coordinates
chr1:261846101-261847817:-
Coord C1 exon
chr1:261847612-261847817
Coord A exon
chr1:261846140-261847611
Coord C2 exon
chr1:261846101-261846139
Length
1472 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
ATCTGTTTTCTCTGTCACAGAAA
3' ss Score
10.03
Exon sequences
Seq C1 exon
GGCCGGCGGCTAGAAGAGGTGCGGCTCAAACCCATCCTCGCCAGTGCCAAAAGGCACAGCCCAGTAACTGAGGGGGCTGTGGAAGTACGGTACGAGGGCCACTGGAGGCAGGTGTGTGACCAGGGCTGGACCATGAACAACAGCAGGGTTGTGTGCGGGATGCTGGGCTTTCCCAGTCAGGCACCTGTCAACAGCCACTACTACAG
Seq A exon
GTAGGAGCGGCGGGATTGCCAAGTTGAACCTGTGTGTTTATGGATCTGTGTGTACATGTATGTGTGTGTGTATATATGCATGTGTGTGTGTGCGTGTGTGTGTGTGTGCATGTGTGTGTAGTGTAAACCTTTAAGGGTTGCACGTGTATGGTGTGTGTGTATGCATGCATGTGTGTTAATGTATGTGTGTGTGCATGTGTGTGTGCATGCATGCATGTGTGTGTGTCTGTGTATATTCATGTGTATATTTATGTGTGTGTGCATGTGTGTGTAGTGTATGTGTGTATGCACATGTGAGTGTGAGTGCATGTGTGTGTAGTGTAAACCATGAAGGGTTGCACACATGTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACACGCATGCCCAGTATAACCTTGTTGAAGGGTTCAGTGAGATTCTGGAGGGACACATTTCCATTTGATTCTTTCATTTTATACCCCTATCAGTTCTTTCTATTGGGTTGGTGAGCATGGGGTTTACTTCCCGACCACTTCTAGATGATTCTCAGGACATTGTAGTTACTATAGTGTGACCTATCCTGGGCTTGGCTCCATCAGGAACCAGCTCTGGGCCTTGGTTGGGGTGCATGGCCTTCAACCATCCTCTGTGGCAACTCTGTGCTGATCAGGGAACTCCTGCTCTGACCTAGACTGTAATTGGGTTGCATGCAAGCTAGACCTGAGGCGGGGAGTTTGAGTAAAGGAGACATAAAAAATACTCTTAGAAATGTGACCAAGCTGTCACAGAAGATTCCATCAGCTCCATAAACAACCACCACAACCCCTGTCCCACCAGCTGTGTCAGTGACATCCCAAGACATTTCTCAAGGCCCCGCTAAGTCATCTAGCCTGCCCCACTCCTACTAGTTTGCCATGTGTCTTCTAGGCAGTTGCAAGTAAGTCCCTTGCCTCTGGCTAGAGGACTCTGGTTCTGAATAAAGAACATGGTAGGCAGCTCTGGGACTCTGTGGGGATGAAGGGGTCTTGGTCCCCTGGCGCCTCAATACCTAGAAATTGCAAATCAGGCCCTGATGACCTACTCACCACCCTTCAGTAGAACAGCCCTGATGACAGTCCGGGTGGCAATCCCCCAACCCCCAGTGAAGCTCTCCACTTGCACAGTTCCCAGGGGACCTTTCCCAAGTCTCTTCTCTCAGGGACCCCGTAAGGATCCTTTCATCTGTACTTAGGGGCTTGGGGGAGGGCAAGAGCGAGTTGTTTACTCCATGGCAGCCCCCGTGCAGTGAGTGTGATGTGGAAGAGCGGCCAACACTGTATGTGGGGTGGATATCCCATCAGGTTCCTGCCCATCTCCATGTTGAAGTAAACACTGTGAAAACATCTATAAACTATGAAGTCTGCTATAAACGTCTGAACGGAAGTGGGGGCCAGGGAGAGTTCTTGCACCCCTCTACCCTATCTGTTTTCTCTGTCACAG
Seq C2 exon
AAAAGTCTGGAATCTGAAGATGAAGGATCCCAAGTCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015727:ENSRNOT00000021144:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.214
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(43.2=73.9)
A:
NA
C2:
PF0053013=SRCR=FE(11.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGCGGCTAGAAGAGGT
R:
AGACTTGGGATCCTTCATCTTCAGA
Band lengths:
241-1713
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]