HsaINT0091046 @ hg19
Intron Retention
Gene
ENSG00000214402 | LCNL1
Description
lipocalin-like 1 [Source:HGNC Symbol;Acc:34436]
Coordinates
chr9:139877445-139879015:+
Coord C1 exon
chr9:139877445-139878160
Coord A exon
chr9:139878161-139878941
Coord C2 exon
chr9:139878942-139879015
Length
781 bp
Sequences
Splice sites
5' ss Seq
CACGTAAGT
5' ss Score
10.16
3' ss Seq
TTGGGGCTCTTTCTCCCCAGGCC
3' ss Score
10.29
Exon sequences
Seq C1 exon
AGGCCCAGGTCCCCATCCAGGCCAACTTTGATGCCAGCCAGGTGTGCCCAGCCCTGTTTCCTCCTCATCTCCAATGAGTCCTCCCGGCTTTGGTGCTGCACCCCGGGTCCCTGTCCACACCCTCTTTGATCCAGGCTCAGCAGGGCTAGGGGCAGGGGAAACCCCCACCTCACCCGCTCCGTCTGACTGGAGTAGGGGTTGGCTGGGGAAGACTGCAGCCTCCATCCTACCTTTTCAGTTGCATCCCCCAACAATCCCCAGGGCCCAAAATAGGGACAAGTTGGTTGCCTGTGCCTCACTGTCCCCCACCCACCCCACAAAGACCTGTGACCTTGCCACAGCCCCACCCATCCAGCCGTACCCCCTGGGTGCCAGCTGCAGACAGGCCGGTGCTGGGCTGGTGGGGGCCAGTTGCTCATGTACTGAGGCCCCCCTCCCTCAGTTCTGCATCGGGGTCGAGATGTGTACAGCAGCCCCTGCCGTGGCCAGGAAGCAGCTGTGTCGGGGCAGAATGTGGTGGGCTCAGGCCCAGGGCACAGGGGCGGCCTCCCAGCCTTCCCTGCACTTGCCCTGCAGTTCCAGGGCACCTGGTACATGGTCGGGGTGGTGTCAGATGACCAGGACTTCCTGGACTCCAAGGACACCATGAAGATGGCTGTGGTCTTAGTGACCCCCTTGGGGAATGGTGACCTGGCCCTCAAGTTTGGATACCCCAC
Seq A exon
GTAAGTGACCACACGAGCCCATCAGACTCAGCCTCAGAGGATGGCCAGCATGAGGCCACATGAAGGTCCAGAGGGACCATGGTGTCCCCAGCACATTGAGGTCAGACCACGGGTCCTCGACGGCTCTGTGCGGCAGAGCCCCAGATGGCAGCCACACGGAGTCCAGAGGGACCCAGGCCCTGGAGGAAGCACTGCCTGAGGCCTGGTGTTGAGAAAAGTGTCTGCATGTCTGTGTCTGTGTGTGTATCACTGTATGTGGCTGTGTCTCTGTGTATGTGTGTCTATTTCTGCATGTGTGTGTGTCTGTGTGTGCGTGTGTATGCATGTGTGTCTTTGTAGATGTGTACCTCTGAGTGTGTATGTGTGTATCACTGTATGCGTCTGTGTGTCTGTGTGTCTGTGTATCTGTGTCTGGCTGTGTGTGTCTATCTCTGTGTGTGTCTTGTGTGCGTGTCTATGTGTGTGTCTGTCAGTGTGTCTGTGTCTGTGTCTATCTCCGTGTGTGTGCATGTGTGTATGTGTGTGTCTTCTGTGTGTCTGTGTCTGGAAGGGGGACCTGGAGGCCCTGCATTCTAGGCTGTGTGCCTGTGAACAGGTACTTAATACCCACCCCACCCCCAGCAGGAGTGTCCCCACCTCTAAGGTCATCCTAAAGTCCCATGTCCTCTAAGGATTGTGAGGGTGAACAGGGGACCCTGGGCTCAGAGACAGCAAGGTAGGCTCTAGGCCTGGGCGCTGGGCAGGGGTGGCCACTCAGGGGATTGGGGCTCTTTCTCCCCAG
Seq C2 exon
GCCCCATGGCGGGTGCCAGAAAATGGACACGACCTTCACCGAGGGTGCTGTACCGGGGCAGTTCAGCAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000214402-LCNL1:NM_207510:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.077
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=PU(36.4=97.6)
A:
NA
C2:
PF0006118=Lipocalin=FE(22.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGCCAGTTGCTCATGTACTG
R:
AGGTCGTGTCCATTTTCTGGC
Band lengths:
347-1128
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)