HsaINT0091017 @ hg19
Intron Retention
Gene
ENSG00000184925 | LCN12
Description
lipocalin 12 [Source:HGNC Symbol;Acc:28733]
Coordinates
chr9:139848606-139849949:+
Coord C1 exon
chr9:139848606-139848707
Coord A exon
chr9:139848708-139849822
Coord C2 exon
chr9:139849823-139849949
Length
1115 bp
Sequences
Splice sites
5' ss Seq
CTGGTAACA
5' ss Score
4.6
3' ss Seq
GACTCCATCTCCCCCACCAGGCT
3' ss Score
7.15
Exon sequences
Seq C1 exon
GCAGGAGCTGGTTGCTGCCTCCCGGGACGCTGGACCAGTTCATCTGCCTGGGCAGAGCTCAGGGCCTCTCGGATGACAACATCGTCTTCCCAGATGTGACTG
Seq A exon
GTAACATGGTTCACCTGCAGGCATGCTGGGCAGTAGGCACGGGGCCCGCAGGAATGAGTTTGGTTGACCCTAGAGGAGCTGGACCCAGTGTCTACCCAGGGAGCTCAGCCCCAGCCTGCGCTCAGGGGTCTCCAGGCTCCTGGGTCCCTGTGCTCAACCCAGGCTCTGAGCCACCTCCTGCCGCCCCGGGTCCCCTGTCCTGGGCCACCTCCTCCCACCCCGGGTCTCCTGTCCCGGGCCACCTCCTCCCGCCCCAGGTCCCCTGTCCCGGGCCACCTCCCCCTGCCCCTCCCGCCCCAGGTCCCCTGTCCCGGCCCACCTCCTCCCACCCCGGGTCTCCTGTCCTGGGCTACCTCCTCCCACCCCAGGTCCCCTGTCCCGGGCCATCTCCTCCCTCTGGGTCCCCTGTCCTGGGCCACCTCCTCCCCTCACCCATCCCTGCTCACAAGGAGCTTGGACTCATCCCAGGAGGTGCCCTGGACCTCAGCAGCCTGCCCTGGGTGGCAGCCCCAGCCTGACCACTCAGACAGCCGCGGCCCCCAAGGCCTGACTCTTCTTGTGGGAGGGCGAGGTCAGCCTGAGTCCCTCCTCTTCCTGGAGGGATGCCCACCGTGCCCTTCTGATTCCCGCCTCTGGTCCTTTACATGTGCATAACCACATGCACACACACTCACGCATGAGCAAACGTGTACAGACTGGCACATGCCTCCACATGCGAACACCCACTTACACACACGCCACTCACACTGGCACACATGCTGTCTACCCGTGCACAGGCACACGTGCTGGTCTGCACACACCTGCACACACCTGCACACTCGCTATGCCAGGCCTCCTGGGTCTGCAGTGAGTCTGGGGGCCCATGGGGACAGGGACAGGTGAGGGGCTTCCTGAGGACCTGGGGCTGTTGGGAGCCGCTGTGGGCCACATCTTCTGCCCCTTCTCAGCCTCCCTCACCCCAGCCCCTTCCCCTAGACCCACTGCTGGTCCCCTTTCTCCCTCCTGCTTCTCACCTGAAGCCACCTGCCCCTCCTTTGTGCCCTCCCTTGCTTCCTCCTGGGCTCTGTCCCCTGCTCCCCCTTTGTCCTCCATCCCGACTCCATCTCCCCCACCAG
Seq C2 exon
GCTGGTCACCCCAGGCCAGCGTCTGTTGAAGGATGAAGCAGCTCCTGTCCGGCCCAGCCCTGCCTCACAGCTGTGCGAGCTCTGCCCTCCTCAGCTCTCAAACCTGAATAAATGCACCAAGCCCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000184925-LCN12:NM_178536:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(23.4=100)
A:
NA
C2:
PF0006118=Lipocalin=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
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:
GGGACGCTGGACCAGTTCAT
R:
TCTGGGCTTGGTGCATTTATTCA
Band lengths:
206-1321
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)