HsaINT0039481 @ hg19
Intron Retention
Gene
ENSG00000163359 | COL6A3
Description
collagen, type VI, alpha 3 [Source:HGNC Symbol;Acc:2213]
Coordinates
chr2:238303230-238305490:-
Coord C1 exon
chr2:238305370-238305490
Coord A exon
chr2:238303848-238305369
Coord C2 exon
chr2:238303230-238303847
Length
1522 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
ACCAATGTCTTTTTTTAAAGATG
3' ss Score
7.5
Exon sequences
Seq C1 exon
GTTCATATTTGGTGCTTAGACAAATTCAAAATGAGGAAACATCGGCACTTGCCCTTAGTGGCCGTCTTTTGCCTCTTTCTCTCAGGCTTTCCTACAACTCATGCCCAGCAGCAGCAAGCAG
Seq A exon
GTAAGAGCCAGAAACGTCCTTGATTTTGTAAAAAGGAATATCATTCTTTGATTTTAGATCTTAGACATCAGGCACTGACATAGAGCTTAGATATGTTCTTAAGGTAGCTAAGCCATTTATTATAGGATAGTCAGATAGGATAGTTCTAGGATTTATAGGCCTTTTCAGATACTCTTTATCCAGTGAGAGATGACCTATTTTTATTAAAACTTGGGTTTGGTATCTTGGAATTGGCTTGAAAATGATTTGTTTTTACATTGGATGTGAACGGAAAGTTTGTATCTCAAATGTTTTACCACCTGAAGGGACTTTCCACATTTCTGGCATTGGCTGGTCTCTGAGCACATAAAGTAGGGAGAAGTCAATGATTGAGAGTAAAAACTATTTTCCCTGAAAAATACAAAGATCACCCTCTCTCTCTAACTCCAGATGCAGGAAGGCATTTTTCATCTAGGATCCTTGAATCTTTAAGATTTCTGTTTCCCAAAACGAATTAAAAGCATGGGTTCTAATTAACTCTATTAAGAATTTGATTTCAGAGTTTTAGAAAAGTGGGAAATGCTTCATGCATTGCAAGCTGGAAAGGACTCAGGTGGGTCTCCCTCTCCTTGACCCAGAGAGCTTGGCCTCTGAGGGATTCTTCCTCCAGGCCAGGTTGCTCTTAGATGGAGGGAAGTCTAGTGTCACTTCAATGGAAGAAGAACGTGGGTTGGGGCATCAGGTCAGCCTGAGGTAAGTAGAGTCCAGCAGCAAGCCTGGCTCACAGCTGCAGAAGGGCACCTCCTGGGGCCACTGACAGCCTGATACCCTGAGCTCCCACCCTTGAGGGAGAACTGGGTTCATCTGGAAATGAGATAGATAATGTTTGACATCTATGGAGACTTTTCTGGCTCTGAAAAATATGCAGTAACTAATAGAGTACAGTTTGTTCATGCTCAAAAAATCTGGAAAAAATAAGTCTTTTCCCTTCTCTACATTTACACAAGTCCTCCTCGCTTAAAGAACATGTATTTATTATATTTATTTTTCACGCAAATTACCCAAAGCATTGGGGGTTAGTGAATGGAAAATAGCAATTTTTACTTTTCCTTTTTTGTCAAGGCCCGGTTTTGTATTCCAAACTAAAGAATGAATTTATAAAATGATGGTTGGTTGTCTGTGATAAGACTTCCTTCTGGTTTAATCAGGTGGGTCTTGGGGCTCAAACTGCCACAGGGAATCATACTTGAGTTAAAGACAGCCCAGGAAATTGTTTCCCCAATCTGGAGCATGCTACTGGCCCATTCATGATGGTCTCTGAGTATGGAACTTGGGCTAGTGACTGGGCACCAGCAGCTATTGAGTGCATGGGCTCAGGTCCCTGGTTCCCAGGTAAGTGAGTCTACCTTCCTGTATTATCAGTGAGGTGTGAAGTGTTTAGTAGCAGTATAGTGTAAACCAAATTTGTTTAGGAAGGCTTTGCATTGATAGGAAGTAATTGCTTACATAGTAGAAAAATCTAAACCAATGTCTTTTTTTAAAG
Seq C2 exon
ATGTCAAAAATGGTGCGGCTGCTGATATAATATTTCTAGTGGATTCCTCTTGGACCATTGGAGAGGAACATTTCCAACTTGTTCGAGAGTTTCTATATGATGTTGTAAAATCCTTAGCTGTGGGAGAAAATGATTTCCATTTTGCTCTGGTCCAGTTCAACGGAAACCCACATACCGAGTTCCTGTTAAATACGTATCGTACTAAACAAGAAGTCCTTTCTCATATTTCCAACATGTCTTATATTGGGGGAACCAATCAGACTGGAAAAGGATTAGAATACATAATGCAAAGCCACCTCACCAAGGCTGCTGGAAGCCGGGCCGGTGACGGAGTCCCTCAGGTTATCGTAGTGTTAACTGATGGACACTCGAAGGATGGCCTTGCTCTGCCCTCAGCGGAACTTAAGTCTGCTGATGTTAACGTGTTTGCAATTGGAGTTGAGGATGCAGATGAAGGAGCGTTAAAAGAAATAGCAAGTGAACCGCTCAATATGCATATGTTCAACCTAGAGAATTTTACCTCACTTCATGACATAGTAGGAAACTTAGTGTCCTGTGTGCATTCATCCGTGAGTCCAGAAAGGGCTGGGGACACGGAAACCCTTAAAGACATCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163359-COL6A3:NM_004369:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.024
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=WD(100=84.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGGAAACATCGGCACTTGC
R:
TCCAGTCTGATTGGTTCCCCC
Band lengths:
356-1878
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)