RnoINT0084631 @ rn6
Intron Retention
Gene
ENSRNOG00000030708 | Lcn4
Description
lipocalin 4 [Source:RGD Symbol;Acc:1596715]
Coordinates
chr3:5169456-5170316:+
Coord C1 exon
chr3:5169456-5169566
Coord A exon
chr3:5169567-5170214
Coord C2 exon
chr3:5170215-5170316
Length
648 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGA
5' ss Score
6.95
3' ss Seq
TATCTGGCCTTTGCTCACAGGAA
3' ss Score
8.56
Exon sequences
Seq C1 exon
TTTTGGGCCATAATCTCTTCTACATCTATGAAGTTCCAGTGAAGGACCACTACATCATATACACCGAAAGCCATCCATTTCGGAAAATATCCCAAACAGGACACCTCATAG
Seq A exon
GTGAGAAATATCAGAGATCCAACCTCCTGCTTATGACCATTAGCTATTTGAATGCCCAGCAACTATATATAGGCACTGGGAAGTCTAAAGCCACAGCCATGTCCTTTAGCAGTTGTGCATAAGGCACCATGTGGTCAGTATAAATGCTTTAAAATGGTAAGCCGTAGTCTGTGCAGAATTTCCAGTGACATGATCGAATGTGGCCTTGAGCACTGAACAATAGGACAGAAATTTATTGACTTAGTACATACCATGTCTTGGAGGCCTCAGCTTTCATGGCAGGAAGTTCTCAATAACGGCTATGTCCTAAATAAAAAACTTTATAGGCAATGACACCCTCCTTCCAGGAGCAGGAGACAGAATTATTAGTTTCCATGACTGTGACATTTCTTGGGTGCTTAAGATATCACCTATAGGTTTTGTCATACTGTGTGTCCTTATATGTCAGCTATATACACGTCCAGTTGACAAGCTTCCCTACCACCATCCATTTTGCACTTCCACATTGATTCTAAAGGCTCCTCTCTTGTTCCCTTATGCTTCAGACTGAATACTCTTGTTCTGTGCAGTCTTCTTGTCTTTCTGTCAGTGGATTCTAATAGGGATGTGTAGTTATTCTCTTTTTGATTATCTGGCCTTTGCTCACAG
Seq C2 exon
GAAAGTATCCAGAAGAAAAACTGGAGGCCTTGGAAGTATTTAAGGAATTCATACAGCACAAAGGATTTCTCCAAGAAAACATCATTGTGCCTGAGCAGAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030708:ENSRNOT00000046109:4
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=0.000
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(26.8=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(24.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Chicken
(galGal4)
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:
TGGGCCATAATCTCTTCTACATCT
R:
CCTCTGCTCAGGCACAATGAT
Band lengths:
209-857
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]