HsaINT0112664 @ hg19
Intron Retention
Gene
ENSG00000165802 | NELF
Description
nasal embryonic LHRH factor [Source:HGNC Symbol;Acc:29843]
Coordinates
chr9:140350863-140352353:-
Coord C1 exon
chr9:140351859-140352353
Coord A exon
chr9:140350939-140351858
Coord C2 exon
chr9:140350863-140350938
Length
920 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
CTCCTTTTTGTCTCTCTTAGACG
3' ss Score
9.83
Exon sequences
Seq C1 exon
ATCACCTGCTGGCTGATGCCTACTCTGGCCACGACGGGTCCCCCGAGATGCAGCCGGCCCCCCAGAACAAGCGCCGCCTGTCCCTCGTCTCCAACGGCTGCTACGAGGGCAGCCTCTCAGAGGAGCCCAGCATTAGGAAGCCCGCAGGCGAGGGCCCTCAGCCTCGAGTGTACACCATCTCTGGGGAGCCTGCCCTGCTGCCCAGCCCTGAGGCGGAGGCCATTGAGCTGGCGGTGGTGAAGGGGCGGCGGCAGCGGCACCCTCACCATCACAGCCAGCCCCTGCGCGCCAGCCCTGGTGGCAGCCGGGAGGACGTCAGCAGGCCCTGCCAGAGCTGGGCGGGCAGCCGCCAGGGCTCCAAGGAGTGCCCCGGATGTGCCCAGCTGGCTCCTGGCCCCACCCCTCGGGCCTTTGGGCTGGACCAGCCACCTCTGCCTGAGACCTCCGGTCGCCGCAAGAAGCTGGAGAGGATGTACAGCGTTGACCGTGTGTCTG
Seq A exon
GTGAGGGGTTTGTGTCAGGGCATAGACAGGTTTGGGGGTGCATGCCGCTGCCAGGGTCTGACAGCAGCAGCCACTGTGAGGCTTGGAACAGAGAACAGGTGCTCAGGTCACAGCATGCCAGCGGACTCAAGATTAAAACCGGCAGGCTTCTGCTGCGGCCTCCACACCCTATGAGCTGTGAGCTCCCTCAGCTCCTCAGCAAAATCTGCCAGGCCTCACAGTCCGCTTTCGCCCTGCTAGCACCAGGTCAATCAAGGAGTGCTTCCTGGAGGAGGGGGCCTGGGAGGATCTTAAGGGATATGTAGGGAGGAAGCACCGCTTAATCAGGAGACTGGGCTGCCCTCCGAGAGTCCTGGGGAGCTGTTGGGGCCCAGCCAGGCAGTGGGCATCTTTCCCCAGGGTTGTTGAGTTGTGTGGTAGCTTGTCCACCAGGCAGAAAGTCACTCCACTGTCCCCACACTTGGGCATCAGGGAAAGGCTGTGGGGGCCCTCGGAAGGGGACAGCCCTCAGCAAGGTGGTCTCTAGCCTCGGTGAGGGCCTCCAGCTAGAGCATGGGGGCTGCAGAGAAGGCCTCAGAGCCTCTTCTGCCCAAGGGAAACAGACGCATTGTTTTCCTGGGCCTCCTGGAGACAGACTGTGCTTTCAAAGGAATGTTTCTCAAACTTTGGGTGGCCAAAGGGAAAGTTAAGCCAAAAAAATCAAAGCGTCAAGTTACCAAGAGCGTGGTCTTGGTGAGTGAGCAGCAGACATTCGAGCACTGCCCTCTGTGCCCGTGTGGGGATGCCACCCTCCCCCCACCCGCCCTGGCTGCCAGCTTCTGCTGACCCCTGGACCCAGAAGCATCTGCTTCCCAACAGGGAGGGAGAGGCTTCAGGAACCCCTACTTCACCCAGCCACCGCTCCTTTTTGTCTCTCTTAG
Seq C2 exon
ACGACATCCCTATTCGTACCTGGTTCCCCAAGGAAAATCTTTTCAGCTTCCAGACAGCAACCACAACTATGCAAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165802-NELF:NM_001130970:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.926 A=NA C2=0.029
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061222=IQ=PU(42.1=30.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTCGAGTGTACACCATCTC
R:
CCAGGTACGAATAGGGATGTCG
Band lengths:
358-1278
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)