HsaINT0091046 @ hg38
Intron Retention
Gene
ENSG00000214402 | LCNL1
Description
lipocalin like 1 [Source:HGNC Symbol;Acc:HGNC:34436]
Coordinates
chr9:136982993-136984563:+
Coord C1 exon
chr9:136982993-136983708
Coord A exon
chr9:136983709-136984489
Coord C2 exon
chr9:136984490-136984563
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:ENST00000408973:1
Average complexity
IR
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
Mouse
(mm9)
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