RnoINT0086078 @ rn6
Intron Retention
Gene
ENSRNOG00000015727 | Loxl4
Description
lysyl oxidase-like 4 [Source:RGD Symbol;Acc:1308588]
Coordinates
chr1:261835992-261838461:-
Coord C1 exon
chr1:261838350-261838461
Coord A exon
chr1:261836635-261838349
Coord C2 exon
chr1:261835992-261836634
Length
1715 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
GATTTTGCTTTGGCCCACAGGAG
3' ss Score
8.28
Exon sequences
Seq C1 exon
GTGGTTGTGAACCCCACAAATGATGTGGCAGAATCAGACTTCTCCAACAACATGATTCGATGCCGCTGCAAGTATGACGGGCAGCGAGTCTGGCTGCACAACTGCCACACAG
Seq A exon
GTAATGCGGCCACAGTGACATCAGCCTTGTATAGCCGATGGGGCTGGGAAAAAGAGGTATACCTGGGTGTGGCTCGTGTGTCACAGATGGCCACGGGTAGGATGACATTGGTCATTAGCCTCCCCACCTAGCAACTACAATCCTTCATGAATGAATGCCTAGTTTCCAGTCTCAGAATCTCCTGTCCTCTCAAGCCACATCAAGATTTTTTTTCCTGCCTGGGTGTGGTAAAAGTGTAAGTCTTGAATCCTGGCACTTGGGGAGGCACAGGCAGATCTCTTGAGTTTGAGCCCAGGATAGCCAGAGCTATGTAGAGAAACTCTGTCCCAGGAAAAGCTTCTCCTTGACCTCTGCCGTTACCTCCAGCTACAAACAGCAGCAGCAGAGGACTGTAGTGTCAGATTGGCCTGGGAAGGAAGGAGCTTCTCTCTGCACAGAATCCCATCTCACGGTTGAATGGTGCCTAGACTTGCTAAGGTCTATGTATTTAAGGTGGGGGGCAGGGCTGGCCTGTCAGTGCGTTTGAAGACCTACAACTGTATTGATCACACTATCACACAGGAGTTCCCCTGGAACTGATGTTATAGGCCACTGTAGGCCCACAGTGTGAGTGCTGGGAACCAAACTCAGGCCCCCCAAGAGCAGTGTACAACTAAACTGCTGAGCCATGCCTCCAGCCTCAGGCTTTGTTCTTAATTAAAATTTTCTGTAATTTGCAACAGGTATGTGCAGTTCAGCTAGCCTTTAACTTGGGCAGTCCTCAGCCTCAGCCTCTACGTTCAGGGATTACTGAGTACAGGCATGTTCCAGTATGCCTGGGTAGTTTCCTTTTGTAAAAATGGACTGTGAGCTTCTAGTTCACTGAGGTGCTCTCTGGAGAGGGGCAATGGGAGGTCTGGGTTGTGACAGAAAAGCACTCCCTGGTCTCAACTCTGAGGCAGGGACACTGACAAAATTTCAGTCAAGATGCAAAGTTTGCTTTTGTATTTCGTCTGTGGTAGTGGGCTCCCACATGCAGGGCCTTCCACGGCTGGGCAGGCACCCTATCACTGAGCTCCATCCCTAGCCTCATTTGTTTTAAAAATAAACTCTGCCAGCAAATGGGAGGGAATGAGAAGGAACGTTTAAGTTTCACATCTGGGTAACTAAGTAGACTTTGCTGACAGAGAACGAAACATGAATGTGAGAGGAATTCGGACTCTGCTTGTGGAGACGACAGAGCCTCCATAACCAGACTGCTAGGGACACACAAAGATAGTGCCAGAGTCCTTCCTTCCACACTCGGTAGTACTCGCTGCAATGCACCTGAAACTATGTGACAAGAGCTCCTTTGAGGACCAGTTAACAAATGACACTGAGCCCAGGGATAAAGGCACGGGGAACTACTGTCCCTGTAAGCTTTTAGGGTAAGGGGTACTTTTAGGGTAAGGGGTACTAGGAGCCAGCGAGCGCCATGGTGGAGGATGAAGCTGGCTAGAGCTGCAGTCTCGGACAATCCCTGCCACTGCAGAGCCTCCTGTTGCTGTTGAGTTACAAGGGGGAAATGAGGGGACAAAGCAGGTAGGGTGGCCACAAAGGAAGAACCTGGGGACTGGGGGGAACAAAGAAGAACCAGTATGGCCCTTTTCACACAACAGGCTGTATGCCTAAGACTGCCCGGATGGAAAGGGGCTGTGGTGGGTTCGTCTACTTAACGATTTTGCTTTGGCCCACAG
Seq C2 exon
GAGATCCCTACCGACCCAATGCAGAGCTCTCCCTGGAGCAGGAACAGCGACTCAGGAACAACTTGATCTAAAGCCGTTATTGCACGCCCCCAGCTCCGCTCACACACCAGATACCTCAGCTTACTGGAGCCATGCCCTTCACAAAGCCCTGACTCACAGGACAAGGGGCCAGTGACAAGGAGCACCAAGAAGCTGCTCAGGAAGCCTTTCAGTGGCCAGATCATCACCGGGATGGCAGTACTCTCAGGACGGCTCTGGCCCCTCCAGAGCACTTATGGCCTAGATAGCATGGCCTTGAGGCTCTGACCAGCTAAACCTTCTCTTCCTTAAGGAGACTCGACCTTTCTTACAACTTGATGCACAGTTCCCAGCTTCAGGAGCTCCAAGTTCCTCAGGGATGAACTGTGACCAAGGTCCTCCCTCTCTAAGTGGTGCTTCACAAGTGTCTTGGAGGAACACAGGACAGAGGAGCAGAGAACACAAGAAGTGGATGGAGTCAGTCCTCTCTGCTATGTGCTCCATGCAAAATAACCATGTCAAAGTCACACCTGGCAGAGAGGCTGGTGAATGCAGTCCCTCTGCTTATCCTCCCTCAGAGGCTCTGAAGCCTCTCCTTGGCAGTTTTACCACACACACACACACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015727:ENSRNOT00000021144:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.130
Domain overlap (PFAM):
C1:
PF0118612=Lysyl_oxidase=FE(18.1=100)
A:
NA
C2:
PF0118612=Lysyl_oxidase=PD(1.0=8.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAACATGATTCGATGCCGCT
R:
AGGCCATAAGTGCTCTGGAGG
Band lengths:
347-2062
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]