HsaINT0113497 @ hg38
Intron Retention
Gene
ENSG00000087303 | NID2
Description
nidogen 2 [Source:HGNC Symbol;Acc:HGNC:13389]
Coordinates
chr14:52010876-52011683:-
Coord C1 exon
chr14:52011554-52011683
Coord A exon
chr14:52011048-52011553
Coord C2 exon
chr14:52010876-52011047
Length
506 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
TGACTTTGCTTTATTTCCAGGTC
3' ss Score
10.19
Exon sequences
Seq C1 exon
GGCTCCATAATCGTGGGAATTGATTACGACTGCCGGGAGAGGATGGTGTACTGGACAGATGTTGCTGGACGGACAATCAGCCGTGCTGGTCTGGAACTGGGAGCAGAGCCTGAGACGATCGTGAATTCAG
Seq A exon
GTCAGCAGCTTCACTCAGCAGTCTGCATTTCATTTGATTCTACAAAGTCACTTGTCTACTTTACGCCGAAGTCTCCCCTCGATTTTTCTCCATTAGGGGAGGTTAAGTTCTAGGCAAGTCATTTTATTGAGCTGTATAAGACTAGCCCCCTCTGTAAGCAAACACCTTCATACATACGGAATGAAATAGGTGATTCCTACTGTGCGCACTTCTTAAAAGAATTCATGGTAAGAATTCAGGGTGACGCCTTCGTTTATTCAGCCTGGCTCTGGCACTGTGGATGCCGGTTGTCATCAAACTGGTAGGTCTGCTGGTCTAGAAGCTAGAGGTAGTGGAATATGTAACAAAAGTACTTGTTTCTCTATTAACCTGGTTCTTGGGGACTTGGAGACACTTGGGCTTTGCTTTCCCCTGCTGACCCCCCTGCCCACCCGACCGTTGGAGGGCTTCAGGTTTGCCCTCCATATCCTGCAAACACTCCAGTCCTGACTTTGCTTTATTTCCAG
Seq C2 exon
GTCTGATAAGCCCTGAAGGACTTGCCATAGACCACATCCGCAGAACAATGTACTGGACGGACAGTGTCCTGGATAAGATAGAGAGCGCCCTGCTGGATGGCTCTGAGCGCAAGGTCCTCTTCTACACAGATCTGGTGAATCCCCGTGCCATCGCTGTGGATCCAATCCGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000087303:ENST00000216286:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PU(71.4=68.2)
A:
NA
C2:
PF0005812=Ldl_recept_b=PD(26.2=19.0),PF0005812=Ldl_recept_b=WD(100=70.7),PF0005812=Ldl_recept_b=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTCCATAATCGTGGGAATTGA
R:
GATTGGATCCACAGCGATGGC
Band lengths:
297-803
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development