HsaINT0039594 @ hg19
Intron Retention
Gene
ENSG00000206384 | COL6A6
Description
collagen, type VI, alpha 6 [Source:HGNC Symbol;Acc:27023]
Coordinates
chr3:130281912-130284458:+
Coord C1 exon
chr3:130281912-130282508
Coord A exon
chr3:130282509-130283837
Coord C2 exon
chr3:130283838-130284458
Length
1329 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGC
5' ss Score
7.93
3' ss Seq
GTTTATTTCTTGCCACACAGCTT
3' ss Score
6.01
Exon sequences
Seq C1 exon
GCCCTGAGTATGCAGATGTTGTGTTTTTGGTGGACAGCTCTGATCGCCTGGGATCCAAGTCCTTCCCATTTGTGAAAATGTTCATCACCAAAATGATCAGCAGTCTCCCCATAGAGGCCGACAAATACCGTGTGGCCCTGGCCCAGTACAGTGATAAACTTCACAGTGAATTCCACCTGAGCACCTTCAAAGGCAGGAGCCCCATGCTGAACCACCTAAGGAAGAACTTTGGATTCATTGGCGGGTCCCTGCAGATAGGAAAGGCTCTTCAGGAGGCTCACAGGACTTATTTCTCTGCACCCGCAAATGGGAGAGACAAGAAACAGTTTCCCCCAATTCTAGTGGTCCTGGCTTCATCTGAGTCTGAGGATAATGTGGAAGAGGCATCAAAGGCCCTGCGGAAAGACGGAGTGAAAATCATCTCTGTAGGGGTGCAGAAAGCTTCTGAGGAAAACCTGAAGGCCATGGCCACGTCTCAGTTTCATTTCAACCTTCGGACAGTCAGAGACCTCAGCATGTTTTCCCAAAACATGACACACATCATCAAGGATGTAATAAAGTACAAGGAGGGAGCAGTTGATGACATCTTTGTAGAAG
Seq A exon
GTGGGCTTAGGATATGTGTATAGGAATGATGATAAAACGCTTTTGAAAAATTAAAATGGGGAGAGGATTGAAATTCTATGAATATTCCTATCCCCAAAATGGGCTGCATTTTCAGATGTTATGTACCCATCGTTTAAGAGAGTCCAGTGATTATGACCATTTTCAATTCAGTGAAGCCCAGAAGTCTTGGTTTTTCATGTTTCACTTATCTGTGTTGCCTGACATTCACAGACTTCTTAAAATTTAGGGATGCTTTCTCCCTGCCACCCAGCTGATCTCTGAGCTATTTCCCTGGGCTTTAGTTGCTATGTAGTTTTAGTACTGGTTCATTGAAAAGGTAAGTTTGCTTCTAAAGAAATTCTTGACTCTTAAAACCACATAATATAATCATAGAATGTTAGACCTAAAGGCAACTTCCAGAAGTCCAGATCCCCCTGTTTTTTTGCAAAAAAGAACTTATATATATCCTTAGAAGTGATGTGCCTTGGCCCAGGGGCCAGGCTGTGACTTAAAGTCAGAGCTAACAGGCCAGATCTCCCAATTCCCAGCCATGTAGTTTCAGCTCCAGACTGCCTTGCTTCCTGCTGCCCTGTTCTGAATTAGTTTTCCCTGTGTTCTGATCTGTGGCCAAACTTCTCTCCTGGTCTGTCCTCTTGTACTACTCTAGTAACAAGAATGGTCAAGAGTTGGTGATCATCATTCAAGTGAAGGGCAGGGGATAGCCAGTAAAAAACAATGTGTTCAAAGTGTACATGTCCAAATATGTTATATAGGAAACTCACATTATCCCTGATTAAATCAGTTTGAATGAGCTGATATATATACTTACCTATTGATAATAGAGAATGCTTTCCTTGGGGTCATCTGTGAAACTATGAGTCCTTATTACTAGCATCATTCCCAAATAAAAGAACTGAAAATGCAATTGCTATTTCGTTACTATCCCTTAGGAATATTTGGACTGTAACTGCTGACTATAGTGTGGATGATGCTTAAATGATTTTAATATGATAGCAATGGCTATGGTTCACTGAATGAATTTTATGTACCAGGCCCCATGCTAAGAATATTGTCGCATTAAATCCCCATAACAACTCTATGAGATTAATATTGTCTCCCTTTTACAGATGAGGAAATTGAAGCCGGGAGTTTAGCTAAGATGTAGTATTTGAACTCAGGTCTCTTTAACCTCAACTTCATAATTATTTGTCTACCTCCTTCTCTAAGTGCATAACTGAGCTCTGCTGTATGGTCTTCATGCCTTCTAATGCTCACCAAAGATGCTGAACCACCAGCTAAAATTGTGCTTGTTTATTTCTTGCCACACAG
Seq C2 exon
CTTGCCAAGGCCCTTCTATGGCCGATGTTGTGTTCCTATTGGATATGTCAATCAATGGAAGTGAGGAGAACTTTGACTATCTTAAAGGATTCTTGGAAGAAAGTGTATCTGCCCTTGACATAAAGGAAAATTGCATGAGGGTTGGCCTTGTGGCCTATAGCAATGAGACAAAAGTGATAAATTCACTGAGCATGGGCATAAATAAGTCAGAGGTTCTCCAGCATATACAGAACCTTTCTCCCCGAACTGGGAAGGCCTATACTGGAGCTGCCATCAAAAAGCTCAGGAAGGAAGTTTTTAGTGCACGGAATGGCAGTCGGAAGAATCAGGGGGTGCCCCAGATTGCCGTGCTGGTGACCCACCGAGATTCAGAAGACAACGTGACAAAAGCAGCTGTTAACCTCCGACGGGAGGGTGTGACCATCTTCACCCTGGGCATAGAGGGCGCCAGCGACACCCAGTTGGAAAAGATAGCATCCCACCCTGCTGAGCAGTATGTCTCCAAACTGAAGACCTTCGCTGACCTGGCTGCTCACAACCAGACATTTCTGAAGAAGCTGCGGAACCAAATAACACACACAGTCTCTGTCTTTTCAGAGAGGACTGAAACGCTCAAATCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000206384-COL6A6:NM_001102608:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.038
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=87.5)
A:
NA
C2:
PF0009223=VWA=WD(100=86.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTTCAGGAGGCTCACAGGA
R:
CCATAGAAGGGCCTTGGCAAG
Band lengths:
354-1683
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)