RnoINT0084614 @ rn6
Intron Retention
Gene
ENSRNOG00000028730 | Lcn12
Description
lipocalin 12 [Source:RGD Symbol;Acc:1589474]
Coordinates
chr3:2718805-2719513:-
Coord C1 exon
chr3:2719354-2719513
Coord A exon
chr3:2718942-2719353
Coord C2 exon
chr3:2718805-2718941
Length
412 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAG
5' ss Score
7.98
3' ss Seq
GCCCATCACCAGCCATGCAGTTT
3' ss Score
-2.8
Exon sequences
Seq C1 exon
ACACCTCGGTCAGGCTATGTCCCTCTGGAGTCTGGTGGCTGTTGGGATGGGACCTTGGTGGGCTCTGTGGCTGATACTCACCCTGCCCCAAATTTTGGGGGGTCAGAGCCCAACCATGCCTCAAGGCTTTTCCCAGATGACGAGCTTCCAAAGCAACAAG
Seq A exon
GTATAGGGCTTTCAAAGGAGAGGAACAGGTTGCACTGACTAGGGTCCCAGCTTGTGGAGGGAGGGAGGGAGCGTGCAGGCCTGTGTGCACTGCTCAGGGAGGCCAGGGCGGAACCTGAACTAAGAGTGAGCCCATGACCTTCAGCAGAACAGGGCCTGGGACCCCCGTAACTTTCTGTATTTGCACGGATCGCTTCCTCTGTGTAAGGAGACAAGCAGAGACTGGGGAATCCCACCCGGCTCCTGAGCAAGGCCACTCTCTGCCTGCCACATCAAAGGCAGATTGAGGGTCTGCCAGTGGCACTGATGCAGCCCTGGCCTGCAGTTGCCTGCTGAAGAGGGGTCCTGACTGGCCATGGGCTGCCCAGGCCAGGGTGGGCAGGGGCTGCCTGTGCCCATCACCAGCCATGCAG
Seq C2 exon
TTTCAGGGGGAGTGGTTTGTCCTCGGTCTGGCAGACAACACCTACAAGAGAGAGCACCGGCCTTTGCTGCATTCCTTTATCACGCTGTTCAAGCTGAGAGACAACAGTGAGTTTCAGGTGACCAACTCCATGACTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028730:ENSRNOT00000020997:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006118=Lipocalin=PU(30.1=95.7)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
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:
CCTCGGTCAGGCTATGTCCC
R:
CGAGTCATGGAGTTGGTCACC
Band lengths:
294-706
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]