HsaINT0039612 @ hg19
Intron Retention
Gene
ENSG00000206384 | COL6A6
Description
collagen, type VI, alpha 6 [Source:HGNC Symbol;Acc:27023]
Coordinates
chr3:130285546-130287448:+
Coord C1 exon
chr3:130285546-130286106
Coord A exon
chr3:130286107-130286890
Coord C2 exon
chr3:130286891-130287448
Length
784 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TCACAGTTTTTCCTATGCAGCTT
3' ss Score
7.32
Exon sequences
Seq C1 exon
GTTGTGTGGACACTGAGGAAGCAGACATCTATCTGCTTATCGATGGCTCAGGGAGCACCCAGGCCACAGATTTCCATGAAATGAAGACGTTCCTGTCAGAGGTGGTAGGGATGTTCAACATTGCTCCCCATAAGGTGCGGGTTGGGGCCGTTCAGTATGCTGACAGCTGGGACTTGGAATTTGAGATCAATAAATACTCCAACAAGCAGGATTTGGGAAAGGCCATTGAGAATATCAGGCAGATGGGTGGGAATACAAACACAGGCGCAGCACTGAATTTCACACTGAGTCTGTTGCAAAAAGCAAAGAAGCAGCGAGGAAACAAAGTTCCATGCCACCTTGTTGTCCTGACAAATGGCATGTCCAAGGATAGCATCTTGGAGCCTGCAAACAGACTGAGAGAAGAGCACATCCGAGTTTATGCTATCGGGATCAAGGAGGCCAACCAAACACAGCTGAGAGAAATTGCAGGAGAGGAAAAGAGAGTGTATTACGTGCATGACTTTGATGCATTGAAAGACATAAGAAACCAAGTTGTTCAAGAAATCTGTACTGAAGAAG
Seq A exon
GTAAGAGAAATCGTGGCTTTACCTACTGACCTTCACTCGCAAATTGCTATCCTGGCAATAATTGACATTGCTGGTTTAGAAAAACAACATAAATTACTAAGTTGAGATTTGTTAACTTGTGTAACTGTGTTCTCTAGAACAAAGCTAAGAGCCCATTATACTGTTGTTCTAAATAATATCTGAAGCATAAGAAAAATATTTGGAGGAATTTCCCTAATAAGTATTAATCAGCTTCCTCTCACAATTTCTTGCCAGGATAGATATATGAGTGTACACCACACGTGTAATATGATAAAATGATTTCAGATTGTAAGGAGTTCTTCAGGTTTATATGAATGTCTTTTTATACAGCTTTTATGAAATCATTTAGAGCTCCTGTTTTCAACCAGGAGTGATTTTGCACCCTTAGAGGTTATTTGTCAACGCCTAGAGACATTTCTGATGGTCATAACTGGAGGGTGCTCCTGTCATCTAAGAGGTAGAGGTCAGGGATACTGCAAAGCATTTTACAGTATCCTACAACACACAGACTTGGCACAGTAAAAATGATACCCAAGATGTCAATGGTGCTGAGGTTGAGTAACCCTGAGTTATGTATTTAAGCAAGTTACTAAATAACAAATAGAATATTCTCACTTTTATTGTCTTCTAAGCTTTATTTACTACTAATTATTACTAAGTACACATGTCAATATAAAATTATTTGTGTTTTGGATTTTCCTGTTTACTCTGAACTTTTTACATGTAGCTGACTTGAATAAACATCACAGTTTTTCCTATGCAG
Seq C2 exon
CTTGCAAAGAGATGAAAGCTGACATCATGTTTCTGGTGGACAGTTCTGGAAGTATAGGACCTGAAAACTTCAGCAAAATGAAAACATTTATGAAAAACCTGGTGAGCAAGTCTCAGATTGGACCAGATCGGGTGCAAATTGGTGTAGTCCAGTTCAGCGACATCAATAAGGAAGAGTTTCAGCTCAACAGATTCATGTCCCAAAGCGACATTTCAAATGCAATAGACCAAATGGCTCACATTGGACAAACCACCCTGACTGGTAGTGCCCTGAGCTTTGTGTCTCAGTACTTCAGCCCCACCAAGGGCGCCCGGCCCAACATCAGAAAGTTTCTCATCCTCATCACGGATGGTGAAGCTCAGGACATAGTAAAGGAACCAGCAGTAGTGCTTCGGCAAGAAGGTGTAATCATCTATTCTGTGGGAGTGTTTGGCTCCAATGTCACCCAGCTTGAGGAGATCAGTGGGAGGCCCGAGATGGTTTTTTATGTTGAGAATTTTGACATTCTGCAGCGCATTGAAGATGATCTTGTTTTTGGAATATGCAGCCCCCGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000206384-COL6A6:NM_001102608:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=92.0)
A:
NA
C2:
PF0009223=VWA=WD(100=90.9)
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:
GGATAGCATCTTGGAGCCTGC
R:
TCGCTGAACTGGACTACACCA
Band lengths:
354-1138
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)