RnoINT0084615 @ rn6
Intron Retention
Gene
ENSRNOG00000028730 | Lcn12
Description
lipocalin 12 [Source:RGD Symbol;Acc:1589474]
Coordinates
chr3:2718047-2718941:-
Coord C1 exon
chr3:2718805-2718941
Coord A exon
chr3:2718124-2718804
Coord C2 exon
chr3:2718047-2718123
Length
681 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
CCTGCCTATCCTTCCCACAGGGG
3' ss Score
12.08
Exon sequences
Seq C1 exon
TTTCAGGGGGAGTGGTTTGTCCTCGGTCTGGCAGACAACACCTACAAGAGAGAGCACCGGCCTTTGCTGCATTCCTTTATCACGCTGTTCAAGCTGAGAGACAACAGTGAGTTTCAGGTGACCAACTCCATGACTCG
Seq A exon
GTGAGTGGGGTGTCTGTCGTGCAAGCAGTCAGGGACTTGGGGCTGTGTTCTGGGAGCCTTGCATGGCCTGGCCACACTGTGGGTTGAGGAACCACATCTGGAGGCCATGTCTAGCACAGCCTGCTTCATGGCCATTGCAAGGCATCTGGTGACTTCCTGTGGCCAGCGTGACTCTTGTGGAGACCCTTGCGGAGCCAGGGACCCTTCTCAGTCTCTGTCTTGGCTCTGCCTGTCCTACCTCGATCTCCTGGGCAGGTTCTTGTTCCTGTGGCAGACATCTCCACTTTGAAGTCTGTCCTTGGCTCTTCTGGAGTTTGTTGGCTCGGGTGCCAGAGGGGGCTAGCGGCTGATACCCAGAAACACTTTCTTTTTAACATGGCAAGTCCCTATACACTTGAGGACCTGTGTATGGGTTGAGCAGGAGTCACTCTTGTGGCACTGGGACAGACTTCTAGGAAGAGCACACAGTAGCTGAAAGATCCTAGAACTGAGGCCGGGGCAACAGCAGGGTTGGGGAGGGGCTCCAGTCTTTTCCATTCTTCTGGGATGCAGATCCCTCCAAATGAACGGCTGATTTTTCTTTTTTCTTTTTTTCTTTTGGTAGTCTACCAGGATGGGCCTGGCTGGCTTCCTAGACCTCTGCCCCACCTCTGTTTCTATTCCTGCCTATCCTTCCCACAG
Seq C2 exon
GGGCAAGCATTGCAGCACTTGGTCCTATACCCTGATCCCAACAAACAAGCCTGGGCAATTCACCAGGGACAACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028730:ENSRNOT00000020997:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.296
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=PU(30.1=95.7)
A:
NA
C2:
PF0006118=Lipocalin=FE(17.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTCAGGGGGAGTGGTTTGTC
R:
CTCTGTTGTCCCTGGTGAATTG
Band lengths:
214-895
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]