HsaINT0074186 @ hg19
Intron Retention
Gene
ENSG00000140511 | HAPLN3
Description
hyaluronan and proteoglycan link protein 3 [Source:HGNC Symbol;Acc:21446]
Coordinates
chr15:89420519-89422500:-
Coord C1 exon
chr15:89422198-89422500
Coord A exon
chr15:89421488-89422197
Coord C2 exon
chr15:89420519-89421487
Length
710 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
TCACGCCCCCTTTCCCCCAGGGC
3' ss Score
10.68
Exon sequences
Seq C1 exon
GTGTGGTCTTTCCTTACCAGTCCCCCAACGGGCGCTACCAGTTCAACTTCCACGAGGGCCAGCAGGTCTGTGCAGAGCAGGCTGCGGTGGTGGCCTCCTTTGAGCAGCTCTTCCGGGCCTGGGAGGAGGGCCTGGACTGGTGCAACGCGGGCTGGCTGCAGGATGCCACGGTGCAGTACCCCATCATGTTGCCCCGGCAGCCCTGCGGTGGCCCGGGCCTGGCACCTGGCGTGCGAAGCTACGGCCCCCGCCACCGCCGCCTGCACCGCTATGATGTATTCTGCTTCGCTACTGCCCTCAAGG
Seq A exon
GTGAGTGGAATAGCCAAGCGCGGGCCTGTGGGTTTGGTGGCCACCTGGGACCTGTGAGAGGGCAGCTTCTGGGGAGCTCTGGCCCCCTCTGCTGGCTCTGCTGGTACTGCCACCTGGAGGCCAAGAGCACCAGCCACCCTAGAAGCAGCATCTGGTTGAGTTTTGAGTGCTTTGCTGCTGCTGCGTTATGCAGGGCATAAATCATTGGTTTCTTCATTCATCAAATGTTTACTGAGTGCCTACCATATGCTGGGGCCTAGACTAGGCTCTCGGGAATCACAGACGAATAAAACACAGCCTGTCTTCACAAAGCAGCTCATTTCGTAGGAAGATGAACAAGTAAAAACAGAAACTGGTTCAGTGTCATATGCCAAGCCCTTGGAAAAGTGTCTGACACATAGTAGGTGTTCAGTAAATGACCGAATGGGCAAGAGACTCTGACTGGTCCAGCCTAGGTGGGGTGCCCACCCACCTAAATAGGGAAGGGTGGTGGGGGAGTGCAGACATGTCTGGAGGGACCTGGGTTCTATGGCAGGTGGGACAGAGCTCTCTGGGACAGGGTGAAGATTAGAAAGTGTTCTCTGCAGATGCCTGCAGTATGGTAGCTCCCTGGGCTCAGACGGGTCTTTGGGGCTGGCATCTCTGCAGACCCCGCTGTGCTCTCTGGCTGCCCCCTGCGCTGTACGGCACTCACGCCCCCTTTCCCCCAG
Seq C2 exon
GGCGGGTGTACTACCTGGAGCACCCTGAGAAGCTGACGCTGACAGAGGCAAGGGAGGCCTGCCAGGAAGATGATGCCACGATCGCCAAGGTGGGACAGCTCTTTGCCGCCTGGAAGTTCCATGGCCTGGACCGCTGCGACGCTGGCTGGCTGGCAGATGGTAGCGTCCGCTACCCTGTGGTTCACCCGCATCCTAACTGTGGGCCCCCAGAGCCTGGGGTCCGAAGCTTTGGCTTCCCCGACCCGCAGAGCCGCTTGTACGGTGTTTACTGCTACCGCCAGCACTAGGACCTGGGGCCCTCCCCTGCCGCATTCCCTCACTGGCTGTGTATTTATTGAGTGGTTCGTTTTCCCTTGTGGGTTGGAGCCATTTTAACTGTTTTTATACTTCTCAATTTAAATTTTCTTTAAACATTTTTTTACTATTTTTTGTAAAGCAAACAGAACCCAATGCCTCCCTTTGCTCCTGGATGCCCCACTCCAGGAATCATGCTTGCTCCCCTGGGCCATTTGCGGTTTTGTGGGCTTCTGGAGGGTTCCCCGCCATCCAGGCTGGTCTCCCTCCCTTAAGGAGGTTGGTGCCCAGAGTGGGCGGTGGCCTGTCTAGAATGCCGCCGGGAGTCCGGGCATGGTGGGCACAGTTCTCCCTGCCCCTCAGCCTGGGGGAAGAAGAGGGCCTCGGGGGCCTCCGGAGCTGGGCTTTGGGCCTCTCCTGCCCACCTCTACTTCTCTGTGAAGCCGCTGACCCCAGTCTGCCCACTGAGGGGCTAGGGCTGGAAGCCAGTTCTAGGCTTCCAGGCGAAAGCTGAGGGAAGGAAGAAACTCCCCTCCCCGTTCCCCTTCCCCTCTCGGTTCCAAAGAATCTGTTTTGTTGTCATTTGTTTCTCCTGTTTCCCTGTGTGGGGAGGGGCCCTCAGGTGTGTGTACTTTGGACAATAAATGGTGCTATGACTGCCTTCCGCCATCCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000140511-HAPLN3:NM_178232:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.074
Domain overlap (PFAM):
C1:
PF0019312=Xlink=WD(100=94.1),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=95.8)
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:
CCAGTTCAACTTCCACGAGGG
R:
GTGGCATCATCTTCCTGGCAG
Band lengths:
345-1055
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)