HsaINT0002219 @ hg19
Intron Retention
Gene
ENSG00000157766 | ACAN
Description
aggrecan [Source:HGNC Symbol;Acc:319]
Coordinates
chr15:89417073-89418585:+
Coord C1 exon
chr15:89417073-89417255
Coord A exon
chr15:89417256-89417635
Coord C2 exon
chr15:89417636-89418585
Length
380 bp
Sequences
Splice sites
5' ss Seq
ACCGTGAGC
5' ss Score
4.78
3' ss Seq
CCATCTCCCTTTCGTCCTAGCCA
3' ss Score
7.26
Exon sequences
Seq C1 exon
TGGCCTGCGGAGAGCCCCCTGTGGTGGAGCATGCCAGGACCTTCGGGCAGAAGAAGGACCGGTATGAGATCAATTCCCTGGTGCGGTACCAGTGCACAGAGGGGTTTGTCCAGCGCCACATGCCCACCATCCGGTGCCAGCCCAGCGGGCACTGGGAGGAGCCTCAGATCACCTGCACAGACC
Seq A exon
GTGAGCATCACCCCGGCCATCTCGCTGAGCACAGGGTTAGATTCTGCCAGCACAGCCTTCCCCCCGTCCCCTCTCCTGGGGACCCTACACCGTCCACAGGGTTGAGCAAGGGAAGGGAGGTCGGGGGGCTGCTCAGTCACAAATAGCTGACCACTGCCCTTAGAAGGGCCACGTACTTGTCCCAGGAGAGGGCTCACTTGGAGGATGAAGGAGAAAAAGCCAGAAAGTCCAAGAAAAATCCAAATCAGGAAAGCCGATAAAGCCTCAGGCGCCTGAGTCCTGGTTTCCACAAGGGAGAGAGGGTAGTCTGGGGAGAGCCTGGGCTCGCCCCACTTTCTTTCCAGGTCCACTGATATCTTTCCATCTCCCTTTCGTCCTAG
Seq C2 exon
CCACCACCTACAAACGCAGACTACAGAAGCGGAGCTCACGGCACCCTCGGAGGAGCCGCCCCAGCACAGCCCACTGAGAAGAGCTTCCAGGACGCACCCAGGACGCTGAGCCCAGGAGCCTGCCAGGCTGACGTGCATCCCACCCAGACGGTGTCCTCTTCTTGTCGCTTTTTGTCATATAAGGAATCCCATTAAAGAAGGAAAAAAATAAATCCCACATTTGTGTATGCACCCACTCACCCCTCCAAATCAGCAAAACCGCATCTAATTTGTCCGCCGAATGCCAAAGCAAAGCAAACTTATTATAACCCTTGGACTGAGTTTAGAGACATTTCTTCAATTTCCCATCGTGCCTTTCCAGGGACCAGTGCAGGGACAGGGGGAGAAGGGGAGGGGTTAAGTTAAATAAAGAAGATTATTTTTGTTTCCTGACTTTATCCAAGAGCAGTGCAATCGTTGGTTATTTCACCTCCAGGGAGAGCTAGGGAGGAGGGAGGAGGGCTCCAAAGGAGCTGGAAGGAGCAGAGGCCTGAGAGCAGGAAGAACTCGGAACCGCAGCTGAATGTATTGGATGAGAAGGAGCCAGGAGGGCTACACCATCTGTATGAGGGAAAAGCCTTGGGGGAGAGGGGTGGGTTCCTGCCTCCTGCCGAGGGTAAGCCGGCAGGAGAGAGCCATCAGAGGGACCTCCGCTGCCTGGGAGTTGGGTTCCCTCCAAGGGTCCCTCTTTCAGTGTCCTCTCTCTCACCTGGGTCTGCCACCCTAACAGGTGGCAACTCGGCAGGGCTGCTGGGGGCACTTCCTGCCCAGTGGGGGGTGCCGCCCAACCTTCTCCCCTCCCCACCCCCGCCCCCGGGACCGTGCAGGCACCAGGGTTCCGTGCACCTATTTATATTTTTGAAAACTGAAGATTATAATATTATAATAATAATAAAGACATTGGAAGAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000157766-ACAN:NM_013227:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.145 A=NA C2=0.888
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACCAGTGCACAGAGGGGTTT
R:
GCTGATTTGGAGGGGTGAGTG
Band lengths:
351-731
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)