HsaINT0091047 @ hg19
Intron Retention
Gene
ENSG00000214402 | LCNL1
Description
lipocalin-like 1 [Source:HGNC Symbol;Acc:34436]
Coordinates
chr9:139878942-139880210:+
Coord C1 exon
chr9:139878942-139879015
Coord A exon
chr9:139879016-139879164
Coord C2 exon
chr9:139879165-139880210
Length
149 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
AGCGGCTCTCGCTCCTCCAGCCA
3' ss Score
7.53
Exon sequences
Seq C1 exon
GCCCCATGGCGGGTGCCAGAAAATGGACACGACCTTCACCGAGGGTGCTGTACCGGGGCAGTTCAGCAACCCAG
Seq A exon
GTGAGGTGGGGCAGCAGGCAGGGCTGTGGCGTGGGGGCCCTGGAGGCTGCATGGACTGCTGGATTGGCACCTGGGGCCGGGGCGTGAGGGGTGCCACGCTCGGGGGGGAGGTGCCCTGGGCCTGGGGTCAGCGGCTCTCGCTCCTCCAG
Seq C2 exon
CCATGGCCCTGAGTGACATCCGAGTGGCCTTCTCCGACTACCAGCACTTTGCCTTGCTGTACTTGGAGATGCGGAAAGGGGGCCTGCGGAACCAGTGGCTGCAGCTCTACGGTGGGCGGGCTGCGGGGCGGAGACCCAGACACCCCCGCTTCGGGTCTGGGATGTCACCCCTGTGCCTGCACCAGCCCTTTCTGCACGCGGAAGGTGGAACCGCTGGCTCCTGGTGTCTGTGGCCGCGGGTCCCGGCCCCTCCCTGCCCCTCTCTCCCTCTCTTCGCCCCTCCAGCCCCTTCCCTTTAGCTTACCCGCCCTCCCCACCTTCAGCTCGAGCGCCCGAGCTGTTTCCCGAAGGCGCCCAGAAGATGCAGCTACTGGCGCCCCAAGTGGGCCTGAGCCCCAGCCAGGGCGTCCTGCTGCCGAAGTCGGGTGAGCGGTGCCGGCAGCCCTGCTGGGAGGGCCAGGCCCCGGGTCACACCCCTGCTGGAAGGGCCAGGCCCTGGTCACTCCACTGATCTCAGATTCGGGACAGAAGTGCCCGGGGCAGACCCAGCCTGTCTGGGTCGGGGGAGGGCGAGACGTTGCCCAGGCCGGTGTTCCCAGGAGGAGATCGCCTTGGGGCAGGTCGGGGGCCTCCGTCCCAGGGAAGGGGGCGCGGGGTGGCGCCTCAGGCTCGATCTCTCTGCAGACCAGTGTGCGGGCGCGCTCTCCCGGGTGAGTAGACCATGGCCATGCGGAGCCGCGGACCATGGGCCCTCCCAGCTCGGTGGGCTGCACCGCGGGGCCCTCTACCTTCGGGGCAGCTAGGGACGACAGCGGGGGTGATGGGGCACCCGGGCGGATCCGAGCCGCAGCAGCCTGGGGAACCGCGGGGCTGCGCGTCGGGAGGGGGCGGAGGCAGGGGACGCCGCCCACCTGCTCCTTGTTTTGCAGTGAGGGGTCCAGCCCCTGAGTGCCCGCAGGGGTCAGCTGCTCCGTGCGCCCAGCCCTGCCCAAAGAGCCCCCTCCCTCCACACCCTGGCCCCAAGCGCAATAAACACCCTGAATGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000214402-LCNL1:NM_207510:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(22.7=100)
A:
NA
C2:
PF0006118=Lipocalin=PD(40.0=44.0)
Main Inclusion Isoform:
NA
Other Inclusion 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:
AAATGGACACGACCTTCACCG
R:
CAGAAAGGGCTGGTGCAGG
Band lengths:
248-397
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)