HsaINT0039475 @ hg19
Intron Retention
Gene
ENSG00000163359 | COL6A3
Description
collagen, type VI, alpha 3 [Source:HGNC Symbol;Acc:2213]
Coordinates
chr2:238270382-238272041:-
Coord C1 exon
chr2:238271896-238272041
Coord A exon
chr2:238270475-238271895
Coord C2 exon
chr2:238270382-238270474
Length
1421 bp
Sequences
Splice sites
5' ss Seq
CTTGTGAGT
5' ss Score
7.15
3' ss Seq
GTTTCTCTTCCTTTCGGTAGGAC
3' ss Score
8.55
Exon sequences
Seq C1 exon
GAGTCCGTGCCTTGATCCTGGTGGGCCTTGAACGAGTGGTCAACTTGGAGCGGCTAATGCATCTGGAGTTTGGGCGAGGGTTTATGTATGACAGGCCCCTGAGGCTTAACTTGCTGGACTTGGATTATGAACTAGCGGAGCAGCTT
Seq A exon
GTGAGTTTTTTTTATGTCTTTATACACAGACCAGTGTAGATACCACACCTTTTGGCATTTCAAGAGAATGAAGTTAATTATCAGCAGGTGAATGGAGGTGGGGGGGGGGCCTTGGTAGATAGTTAAATTTATTTAATTCACTTGGGAACTGCCTTGTTGCCATAACACATGTGAATCTGGAAATGGAGATAGCAAATCGCTGGAAATCCAGCGAGCTGGAAGGGGATCCTGGGCGCGCTGAGGTTGTGGCCTTAGCATTTTCTCTGCTCCCTTAGCAACGGCCTCTTTTAACACCATTGCAGGGATGCAAACCATCGAGATTGTCCATCCTCCAATTGGAAACTGTGTCAAGAGCATCTGAAATCTTGCATGATAAAAACAACATGCAGGAAAAGAAAGGCTGTTTCTGGGTGGAGAAGTGCTTTAATTGCCCTCCCTAGTTTCCCTCTGTGTCAATGAAGCTCCCTCTGAGGCTTCCTCATTCTCCCCAGGGCCAGCCTCTCTCAGCTGGAGGTGTGACCTCCTGGGTTTAGACTGGGGATGGAGCTTTTGGAAGATGTGGGGCTGAGCTGCGAACTCAGAGATTCTTTGATGGTAGCAACAGTGGACTGTGGCTATGAGAATGGGAGGAATGGACCTTCCTTTCTTCCATACTTCTTTGCAGGGTTAGAATCAGGATTTTTTTCCTAGTGGAAGTAGGTTGAGTTAGCTCACAAATCTGGGATATGGGAGAAAGGGAAAGCTCTTGGAAGCTCGTTGGAAGAAAGTGCATGTGCCCACCATTAGTTTAGCAGATGGAAATGTATTTGGGCATGCCCTTTCCCACATAAGGTCAGGGGCCAGATGGGATGAGAATGTAGAGGGTGTCTGTGTGACCTGGAGTTGAGAAGCTTTTGGCTCCGAGGCCAGGACCACTTGTGCCTGCTCCCACCATGGCTGCTCTGGAAGCCTCTTTCTGGGCTGGTACCATATCCCATGACTCTCACCCTGGTTCCAAGGAAGGGTGGTCATGGATATCTGTTCTGGAACCACCTTCAGTCTTGGCCATCTGCCATTTGCTTGGCTTTGCACTTTGGAACTGGAACATATGTAAGTTATAGTTAAGATCTGATGATGGAAACTTCTAGAAATAAGGTCCAGCCTGCAGTGATATTGTGGATAAGATCTATTTTACTTTGGTTGTTCTTTACTTTCCTATTGGTGACCTCCCATCTGCACCCCGACCGCCAGGAGCTGGGCCCTCCTGACTTCGCTGGCAATTTCTATCATATCGTCAGTCGTCCAGCAAATGTCACCTGGAGGGACTTCATCTCACACCGTGAAACCCCCACACATCCGATTTTGACCCTTAAAGCGCATTTATGATTTTCTGCTGGGCATTTCTTGAGATCTGAACATTTGGTTTCTCTTCCTTTCGGTAG
Seq C2 exon
GACAACATTGCCGAGAAAGCTTGCTGTGGGGTTCCCTGCAAGTGCTCTGGGCAGAGGGGAGACCGCGGGCCCATCGGCAGCATCGGGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163359-COL6A3:NM_004369:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.355
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(11.7=36.7)
A:
NA
C2:
PF0139113=Collagen=PU(26.2=51.6),PF0139113=Collagen=PU(2.1=6.5)
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:
GAGTCCGTGCCTTGATCCTG
R:
CTTTGGCCCGATGCTGCC
Band lengths:
239-1660
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)