HsaINT0074190 @ hg19
Intron Retention
Gene
ENSG00000187664 | HAPLN4
Description
hyaluronan and proteoglycan link protein 4 [Source:HGNC Symbol;Acc:31357]
Coordinates
chr19:19366452-19369664:-
Coord C1 exon
chr19:19369332-19369664
Coord A exon
chr19:19369018-19369331
Coord C2 exon
chr19:19366452-19369017
Length
314 bp
Sequences
Splice sites
5' ss Seq
CGGGTGCGT
5' ss Score
7.91
3' ss Seq
CCCCCACCTCACCCCCGCAGGGC
3' ss Score
10.43
Exon sequences
Seq C1 exon
GCGTGGTCTTTCCCTACCACCCCCGTGGAGGCCGATACAAGCTGACCTTCGCGGAGGCGCAGCGCGCGTGCGCCGAGCAGGACGGCATCCTGGCATCTGCAGAACAGCTGCACGCGGCCTGGCGCGACGGCCTGGACTGGTGCAACGCGGGCTGGTTGCGCGACGGCTCAGTGCAATACCCCGTGAACCGGCCCCGGGAGCCCTGCGGCGGCCTGGGGGGGACCGGGAGTGCAGGGGGCGGCGGTGATGCCAACGGGGGCCTGCGCAACTACGGGTATCGCCATAACGCCGAGGAACGCTACGACGCCTTCTGCTTCACGTCCAACCTGCCGG
Seq A exon
GTGCGTAGGCCTCACCCCAAGACTGGCCTCTGCTGCAACACTACCCCAACCCCGGGGCCTTCTTCCCCACCCAGCTCTTAGCGATCAGAAACAGGAGACCCCTCTCCCAAGAGTGCCTAGGCGCAGCACACACCGCCTGGTACCAACGCTGGTTGGGCCTAGGCTGGGGTCCCAGGCTGCAAAGGAGGAACTGTTCCTGGATCCCGGGGCCGAGGCCAGAGTCCTAGGCTGCATGCGGGGGGCAGTCCTGAATCCCACCGAAGCAGGGTCCCAGGAGCCGCACTAATAACCCACCCCCCACCTCACCCCCGCAG
Seq C2 exon
GGCGCGTGTTCTTCCTGAAGCCGCTGCGACCTGTACCCTTCTCCGGAGCTGCGCGCGCGTGTGCTGCGCGTGGCGCGGCCGTGGCCAAGGTGGGGCAGCTGTTCGCCGCGTGGAAGCTGCAGCTGCTAGACCGCTGCACCGCGGGTTGGCTGGCCGATGGCAGTGCGCGCTACCCCATCGTGAACCCGCGAGCGCGCTGCGGAGGCCGCAGGCCTGGTGTGCGCAGCCTCGGCTTCCCGGACGCCACCCGACGGCTCTTCGGCGTCTACTGCTACCGCGCTCCAGGAGCACCGGACCCGGCACCTGGCGGCTGGGGCTGGGGCTGGGCGGGCGGCGGCGGCTGGGCAGGGGGCGCGCGCGATCCTGCTGCCTGGACCCCTCTGCACGTCTAGGCTGGGAGTAGGCGGACAGCCAGGGCGCTTGACCACTGGTCTAGAGCCCTGTGGTCCCCTGGAGCCTGGCCACGCCCTTGAAGCCCTGGACACTGGCCACATTCCCTGTGGTCCCTTACAAACTAACTGTGCCCCTGGGGTCCCTGAAGACTGGCTAGTCCTGGCAGAACAGTACTTTGGAGTTCCCTGGAGCCTGGCCAGCCCTCACCTCTTCTGGATAGAGGATTCCCCCAACTCCCCAACTTTCTCCATGAGGGTCACGCCCCCTGAGGACCTCAGGAGGCCAGCAGAACCCGCAGGCTCCTGAAGACTGGCCACGCCTCCTGAGACCACTTGGAAACAGACCAACTGCCCCCGTGGTCGCCTGGTGGCTGGACCCCCGGGATTGACTAGAGACCGGCCGTACACCTTCTGCATCTCACTGGAGACTGAACACTAGTCCCTTGCGGTCACGTGGGACACTGGGCGCCTCCTCCTCCCCCTCCTCCTCACCTGGAGAGACTACAGGAACTTCAGGGTCACTCCCCGTGGTCACATGGAGGTTGTGGGCCGAGGCGCTTATTTTCCCTTATGGTGACCTGAGTCCTGGAGACTCCCATTCTCCCCCTCTCCCTGAGAGTCCCCTGCAGTTTCTGGGTAACAGGGCACACCCCTCTAGTTTCATGGGCGAGCACCCCCATCTGCCACCTCAGACTGACACACAGCCAGCTGGCTCACTTACTGGGGGCCACGTCCCACCCCTCAGATATTTCTTTGAAGGGAGAGCAAACCCACCCTGTCCTCTGACGTCCCTTTCCCAACTGTCACCAAACAGACCATCTTCCCAGGCCTGGGGACCGGTAAGATCCATGTCACTAGTTATGCAGAGCAGTTGCCTTGGGTCCCACTGTCACCAAGGCAACCAGTCCTGCTGCTACCTGTCACCTAGAGTCACACACCCCTTCCCTCATCAGGCACACCCATGAAGACAGTGCCTCCCTCCTCCAGCTGTAACCATGGATACCACACATTTCTCATCTCATTGGCCCCCACCCCAGAGACCTCCACCTCAACTTCTGGCTGTCCCTACCCTGACTCACCGCCATGGAGATCACCCTCCCCGAAGCTGTCGCCAGGGTGACCCAACATCCAGTTCTCCGGCTCTCACCATGGAAACAAACTGTCCCTGTCCCCAGGCCCACTCCAGTTCCAGACCACCCTCCATGCTCCACCCCCAGGCGGTTTGGACCCCACCACTGTTGCCATGGTGACCAAACTCTGGAGTCCGAGGTAACAGAACACCTGTCCCCCTAGGCTTTTCCTTGTGGACAACGGGGCCCTGTTCACCAAGCTGTTGCCATAGAGACTGTCAACGTTGTCCTCATGACAACCAGACTTCCAGTTCTCAGGAACTTCTCATTGTGGGCCAGAAGTCCTGGGTGCCTCCTACTAGGGCTACCCTACTGCACCCCATCAGGGGCCTGATGGCTGCCCCTTCCCCAGACAGGGCTGGACTTCTGGAGCTGCTAAGCCACCCTCCGTTTGCACGTTAACTCTATGCCGGATAGCAGCTGTGCACGAGACAATCTTGCAACACCCGGGCATGTTTGTCGTCGTCCTACAAATGAGGAAACCGAGCCTATGGCGTGCCCTGGTCTGTTGAGATATGCAAGCACTGAGCTCCTCTTTTGTCCTCTGAGACCCCATCTCCATTCTCACCCAGTTCCTCTCTCCTTCCCTGACCCCCACCCACATTTCCCTCCTTAGAGATCCAGGAGGGATGGAATGTTCTTTAAAATTCAACACCCACCAGGCTCTAAGCGGCGATCTGTGCTAAGAGGTCAGGACCCAGCCGAAGTCCTCGGCGTTGACAGGCAGCTGGGGGGACATGATCCATGGACAAGGCCATCCCGGCCGTGGGAGACCCCAGTCCCGAAGTCTTGCCTGCAGGAGTACTGGGGTCCCCCTGGGGCCCTCTTTACTGTCACGTCATCTCTAGGAAACCTATCTCTGAGTTTTGGGACCAGGTCGGTTTGGGTTTGAATTCTGCCTCTTCTTGCTCACTGTGTGACCAAGTGACAAACTCCTTCTGAACCTGTGTTCTCCCACTGTACCAGGGCTGTTCTGTGGTCCCCGTGAGTGCCAAGCATACAGTAGGGGCTCAATAAATCCTTGTTTCTTTTGATGAATGAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000187664-HAPLN4:NM_023002:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.015
Domain overlap (PFAM):
C1:
PF0768612=V-set=PD(1.7=1.8),PF0019312=Xlink=WD(100=94.6),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=70.2)
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:
GGCCGATACAAGCTGACCTTC
R:
CTCCGGAGAAGGGTACAGGTC
Band lengths:
352-666
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)