HsaINT0039508 @ hg19
Intron Retention
Gene
ENSG00000163359 | COL6A3
Description
collagen, type VI, alpha 3 [Source:HGNC Symbol;Acc:2213]
Coordinates
chr2:238287279-238290142:-
Coord C1 exon
chr2:238289558-238290142
Coord A exon
chr2:238287879-238289557
Coord C2 exon
chr2:238287279-238287878
Length
1679 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
TTTTCTGTGCTTCACTGCAGTTC
3' ss Score
9.27
Exon sequences
Seq C1 exon
TCATTGAAGTCAACAAGAGAGACATAGTCTTCCTGGTGGATGGCTCATCTGCACTGGGACTGGCCAACTTCAATGCCATCCGAGACTTCATTGCTAAAGTCATCCAGAGGCTGGAAATCGGACAGGATCTTATCCAGGTGGCAGTGGCCCAGTATGCAGACACTGTGAGGCCTGAATTTTATTTCAATACCCATCCAACAAAAAGGGAAGTCATAACCGCTGTGCGGAAAATGAAGCCCCTGGACGGCTCGGCCCTGTACACGGGCTCTGCTCTAGACTTTGTTCGTAACAACCTATTCACGAGTTCAGCCGGCTACCGGGCTGCCGAGGGGATTCCTAAGCTTTTGGTGCTGATCACAGGTGGTAAGTCCCTAGATGAAATCAGCCAGCCTGCCCAGGAGCTGAAGAGAAGCAGCATAATGGCCTTTGCCATTGGGAACAAGGGTGCCGATCAGGCTGAGCTGGAAGAGATCGCTTTCGACTCCTCCCTGGTGTTCATCCCAGCTGAGTTCCGAGCCGCCCCATTGCAAGGCATGCTGCCTGGCTTGCTGGCACCTCTCAGGACCCTCTCTGGAACCCCTGAAG
Seq A exon
GTATGGTGGTGATGGCTTCAGACACACAATGGGGTGGTCTCCAGGCAGGGCCTTTAAGAACAAAACAAAATGAAGTGTGTTTGTGTTTAGCTAAGAGACAACAAATGATGAAAACAGCAGCAACGAACATGATTTATTCCAGGTTTCCTTTTGCACTGGGTTCAGGATTGTATGGTTTACAATGTCATGCAATGAAATTTCATATAAGAACCATATGATTTAAACCACAGGACCATGGGCCACCACCTGTCTTTGAAGCTTCTGGCCGAGGAGGTCACATCTCAGTTCTTATCGCTTGTCAGATCCCTGTGTTCTTCTGTTTCTACTGGTGATTTCTGTCCAGTCTCCTCCTCATCACCAGGATGTAGCTTTCCTTTCCTGAGTTGTCCATCTACTTCTAAACAGCCCCAGTCTGAGCTGTTTAGGGCACAGTGTCCTCAGCTTTTAATCCCTCTCTTCTCTCTCGTTAAGGGATTACCCTCAATGGGAAAGCATATTGAATGGCTAAGTGTGGAGTTCAAACCTAGTGGTTCTTCAAATCCCTCATTTAATATGATTGCCAGTGGAGAGTTATTTTTAAAGACATTATACAGATCTATGAGCTAATGAGTTGAAGAAATACAATTCACTGCCCTTAATGAAGAGAAGATGAGCATCACAGAATGATGCTTTCCCACCTTGCAGACTCGATCACTAGAGGATTGCCTGATGCAGGCATGACCCATGCTGCCTGGATGCATGCTTTCTCTTCACACTCCCTGGTCTTCTATATCCATCTCTTTCTCTCTCTTTTAAAATTTTTCTTAAAACTTTTAATCCACACTTTCATAGCCAAAGTTCAACTTAGGATACAATTAGTTGTGAGGTCTAAATTACAGTAGGGCATCAGGGAAGAAATAAAAAATAAAATTTTAAAGGCACATGGTAAATGTGTTGGGTCAAATACACTATTTTGAGAATTATACTTTTTATTCTTGATGTGTATAAGTTTGGCCAAGCCTAGCAACTAGTCTCCTTCTATTTTGCTGTGTATTTACGGTCCCATCATCTCACTTTGGGGGAATTCCCCTGTTGGATGATTGCCTAGCAAGACTGTGACTTCCTAATAGGAGAAGAGTCCCAGTGGAGAATGACAAACGGGGAAGTCTGAAGAAGACTTCAATATGAGACCAGCCTACTTTTGCTATTTTTTTTAGCCTTAAGGAACTCGTTTTCTCAGGTTAGTGAGGGCTAACTGCTTCTGAGCTATGGATGGAAGACCCTCTGTTTGTGGGTAGAGGTGAGCCCCAGAGGATCCAGCCAGGCAAACTTAAACCTGGCTGGGATGAGTGATATGGACTGATGCAGCACCTTCATAGTATTCATTTTTAGGGAAGGAGTGTTTGGTTTCAAGGATTCTGATCACTTTTGTTGTCTGTAAACATTCTAACTTTGATGTTGTAGCTCTCTTTGAGCCAACTTGGTTTTGTAAACTCGGCTACCAATATGTCTCACAAACACCAGCCACCACCAGAGGAAAATATGCAGCCATCTGCCATATTTTACAAGATGGACATGCTTTGCCATGCTGACTTTCTCTGTGTTCTAAATGTTGGCATGTGTGCACGTGTTGTAGGCACACATGATAAAACTCTCCGTGGTTGTGTATGTCTCACTTTTTTTTCTGTGCTTCACTGCAG
Seq C2 exon
TTCACTCAAACAAAAGGGATATCATCTTTCTTTTGGATGGATCAGCCAACGTTGGAAAAACCAATTTCCCTTATGTGCGCGACTTTGTAATGAACCTAGTTAACAGCCTTGATATTGGAAATGACAATATTCGTGTTGGTTTAGTGCAATTTAGTGACACTCCTGTAACGGAGTTCTCTTTAAACACATACCAGACCAAGTCAGATATCCTTGGTCATCTGAGGCAGCTGCAGCTCCAGGGAGGTTCGGGCCTGAACACAGGCTCAGCCCTAAGCTATGTCTATGCCAACCACTTCACGGAAGCTGGCGGCAGCAGGATCCGTGAACACGTGCCGCAGCTCCTGCTTCTGCTCACAGCTGGGCAGTCTGAGGACTCCTATTTGCAAGCTGCCAACGCCTTGACACGCGCGGGCATCCTGACTTTTTGTGTGGGAGCTAGCCAGGCGAATAAGGCAGAGCTTGAGCAGATTGCTTTTAACCCAAGCCTGGTGTATCTCATGGATGATTTCAGCTCCCTGCCAGCTTTGCCTCAGCAGCTGATTCAGCCCCTAACCACATATGTTAGTGGAGGTGTGGAGGAAGTACCACTCGCTCAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163359-COL6A3:NM_004369:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=87.2)
A:
NA
C2:
PF0009223=VWA=WD(100=88.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTATTCACGAGTTCAGCCGG
R:
CAACGTTGGCTGATCCATCCA
Band lengths:
347-2026
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)