HsaINT0091047 @ hg38
Intron Retention
Gene
ENSG00000214402 | LCNL1
Description
lipocalin like 1 [Source:HGNC Symbol;Acc:HGNC:34436]
Coordinates
chr9:136984490-136985761:+
Coord C1 exon
chr9:136984490-136984563
Coord A exon
chr9:136984564-136984712
Coord C2 exon
chr9:136984713-136985761
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
CCATGGCCCTGAGTGACATCCGAGTGGCCTTCTCCGACTACCAGCACTTTGCCTTGCTGTACTTGGAGATGCGGAAAGGGGGCCTGCGGAACCAGTGGCTGCAGCTCTACGGTGGGCGGGCTGCGGGGCGGAGACCCAGACACCCCCGCTTCGGGTCTGGGATGTCACCCCTGTGCCTGCACCAGCCCTTTCTGCACGCGGAAGGTGGAACCGCTGGCTCCTGGTGTCTGTGGCCGCGGGTCCCGGCCCCTCCCTGCCCCTCTCTCCCTCTCTTCGCCCCTCCAGCCCCTTCCCTTTAGCTTACCCGCCCTCCCCACCTTCAGCTCGAGCGCCCGAGCTGTTTCCCGAAGGCGCCCAGAAGATGCAGCTACTGGCGCCCCAAGTGGGCCTGAGCCCCAGCCAGGGCGTCCTGCTGCCGAAGTCGGGTGAGCGGTGCCGGCAGCCCTGCTGGGAGGGCCAGGCCCCGGGTCACACCCCTGCTGGAAGGGCCAGGCCCTGGTCACTCCACTGATCTCAGATTCGGGACAGAAGTGCCCGGGGCAGACCCAGCCTGTCTGGGTCGGGGGAGGGCGAGACGTTGCCCAGGCCGGTGTTCCCAGGAGGAGATCGCCTTGGGGCAGGTCGGGGGCCTCCGTCCCAGGGAAGGGGGCGCGGGGTGGCGCCTCAGGCTCGATCTCTCTGCAGACCAGTGTGCGGGCGCGCTCTCCCGGGTGAGTAGACCATGGCCATGCGGAGCCGCGGACCATGGGCCCTCCCAGCTCGGTGGGCTGCACCGCGGGGCCCTCTACCTTCGGGGCAGCTAGGGACGACAGCGGGGGTGATGGGGCACCCGGGCGGATCCGAGCCGCAGCAGCCTGGGGAACCGCGGGGCTGCGCGTCGGGAGGGGGCGGAGGCAGGGGACGCCGCCCACCTGCTCCTTGTTTTGCAGTGAGGGGTCCAGCCCCTGAGTGCCCGCAGGGGTCAGCTGCTCCGTGCGCCCAGCCCTGCCCAAAGAGCCCCCTCCCTCCACACCCTGGCCCCAAGCGCAATAAACACCCTGAATGCCTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000214402:ENST00000408973:2
Average complexity
IR
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
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:
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