HsaINT0074182 @ hg19
Intron Retention
Gene
ENSG00000132702 | HAPLN2
Description
hyaluronan and proteoglycan link protein 2 [Source:HGNC Symbol;Acc:17410]
Coordinates
chr1:156594393-156595517:+
Coord C1 exon
chr1:156594393-156594575
Coord A exon
chr1:156594576-156594892
Coord C2 exon
chr1:156594893-156595517
Length
317 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGG
5' ss Score
8.48
3' ss Seq
TGACCCGCTGTGGTCCCCAGGCC
3' ss Score
9.14
Exon sequences
Seq C1 exon
CTTGGACCGAGGGTCTGGACTGGTGTAACGCGGGCTGGCTGCTCGAGGGCTCCGTGCGCTACCCTGTGCTCACCGCACGCGCCCCGTGCGGCGGCCGAGGCCGGCCCGGGATCCGCAGCTACGGACCCCGCGACCGGATGCGCGACCGCTACGACGCCTTCTGCTTCACCTCCGCGCTGGCGG
Seq A exon
GTGAGGCGCGGGACGAAGGCAGGGTCTTGGGGAGGGGTCTGAAAAATGTGGGGGACGAGGAGTGGACCTCAGCTTGAGATCAGGGCAGGGTCTCCGGGTCCCTCCAAGGCACCGCCCCCCCATCAGCCCGCCCGCCCGCCCAGGCTCCAGCTCACCTCTCCAAACCCTCCCTGCACTTTTGCCTCGATCCCCCAACTCCTCTTACCCAAGCTCGATCCAGCACCTCTGCGGTCCCGCACCCCAACTCCGCCTCCTGGGTGTCAGCCGCCCCTCTCCGCCCACCCTGCCCTCGGTCGGTGACCCGCTGTGGTCCCCAG
Seq C2 exon
GCCAAGTGTTCTTCGTGCCCGGGCGGCTGACGCTGTCTGAAGCCCACGCGGCGTGCCGGCGACGCGGCGCCGTGGTGGCCAAGGTTGGGCACCTCTACGCCGCCTGGAAGTTTTCGGGGCTAGACCAGTGCGACGGCGGCTGGCTGGCTGACGGCAGTGTGCGCTTCCCAATCACCACGCCGAGGCCGCGCTGCGGGGGGCTCCCGGATCCCGGAGTGCGCAGTTTCGGCTTCCCCAGGCCCCAACAGGCAGCCTATGGGACCTACTGCTACGCCGAGAATTAGGCGCCCACCGTGTCCCCTCCAGCGCGCGCGAAGAAGCTTGGGAGTCGTGGCGGGGGTCTCTCGCCACCCCTTTCCGGAGAGCCTCCCCTCCCTCCAGACCCGGAGCGGCCTCTCCAGACCTGCCTTCCCAGCCGGGGGCTGCGGGCCTCGGACCCCGGCTGGCCCGGCGGCGGGGAGGGGAGGCGGGGGCGCCTCCGGCGGCGAGATGCAGAGGTGACCCTCGGACCCGCTGCCGTTCGCGAACCCTAGCAGAGGACTCAGCCACCGCCGGGGGGAGGGTGAGGCGGCCGGGGGCATTAACTGACCTCTGAGTACAGCAATAAAATAACCTGGGGATCTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000132702-HAPLN2:NM_021817:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PD(57.9=88.7),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=95.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGAGGGTCTGGACTGGTGTAA
R:
TGATTGGGAAGCGCACACTG
Band lengths:
350-667
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)