HsaINT0113504 @ hg19
Intron Retention
Gene
ENSG00000087303 | NID2
Description
nidogen 2 (osteonidogen) [Source:HGNC Symbol;Acc:13389]
Coordinates
chr14:52520297-52521039:-
Coord C1 exon
chr14:52520738-52521039
Coord A exon
chr14:52520657-52520737
Coord C2 exon
chr14:52520297-52520656
Length
81 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGGA
5' ss Score
6.45
3' ss Seq
GCCATTCTATCCTGAAACAGAAT
3' ss Score
6.16
Exon sequences
Seq C1 exon
ACTAAGCAACCTGGGGATCCCTGGAGTGTGGGCTTTCCATATCGGCAGCACTTCCCCGTTGGACAATGTCAGGCCAGCTGCAGTTGGAGACCTTTCCGCTGCCCACTCTTCTGTTCCCCTGGGACGTTCCTTCAGCCATGCTACAGCCCTGGAAAGTGACTATAATGAGGACAATTTGGATTACTATGATGTGAATGAGGAGGAAGCTGAATACCTTCCGGGTGAACCAGAGGAGGCATTGAATGGCCACAGCAGCATTGATGTTTCCTTCCAATCCAAAGTGGATACAAAGCCTTTAGAGG
Seq A exon
GTAGGATCTCCCCTCCAGATTCTGATCTGTCCTCCCCCTTGCATCCAACACCTACTTATTGGCCATTCTATCCTGAAACAG
Seq C2 exon
AATCTTCCACCTTGGATCCTCACACCAAAGAAGGAACATCTCTGGGAGAGGTAGGGGGCCCAGATTTAAAAGGCCAAGTTGAGCCCTGGGATGAGAGAGAGACCAGAAGCCCAGCTCCACCAGAGGTAGACAGAGATTCACTGGCTCCTTCCTGGGAAACCCCACCACCGTACCCCGAAAACGGAAGCATCCAGCCCTACCCAGATGGAGGGCCAGTGCCTTCGGAAATGGATGTTCCCCCAGCTCATCCTGAAGAAGAAATTGTTCTTCGAAGTTACCCTGCTTCAGGTCACACTACACCCTTAAGTCGAGGGACGTATGAGGTGGGACTGGAAGACAACATAGGTTCCAACACCGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000087303-NID2:NM_007361:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.569 A=NA C2=0.950
Domain overlap (PFAM):
C1:
PF061199=NIDO=PD(17.9=16.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
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:
GGTGAACCAGAGGAGGCATTG
R:
CTCTCTCATCCCAGGGCTCAA
Band lengths:
181-262
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
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)