HsaINT0039488 @ hg19
Intron Retention
Gene
ENSG00000163359 | COL6A3
Description
collagen, type VI, alpha 3 [Source:HGNC Symbol;Acc:2213]
Coordinates
chr2:238259773-238261227:-
Coord C1 exon
chr2:238261165-238261227
Coord A exon
chr2:238259836-238261164
Coord C2 exon
chr2:238259773-238259835
Length
1329 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
3' ss Seq
TTCCTCCCCTCCTGCTCCAGGGA
3' ss Score
10.21
Exon sequences
Seq C1 exon
GGCCCAGCTGGTCCTGCTGGTCCTCCAGGGCTGATAGGAGAACAAGGCATTTCTGGACCTCGG
Seq A exon
GTAAGCCTGTCCTAATACCAGCCCCCTCTCTAGCTGAACAGAGGGCACATTGCCAAGCAGGCTGAGAGAGTTTCTCGGATGATGCTATTGTAGACAGACCTCCCTTTAGCTCTCCTCTTTGGCAACAAAAACCCCAGATTTAACCTCAGGCCTTGCAGTGACTGGCTACTTCACCCCAAGAAAGTAAGAGTTTCCTTTTTTGGTGCTCCATGGGCCTCTAAGTCTCAATTCTGCTCCTTCCAAGTGTCCCTGGGTGGAAATCAGGGGATATGCCTCAGGATGGAATCCTGGAAAATCTAAATCTACCAAAATGCTTAGATTCTGCAAGGTGTTTCCCCTTTGGTCCCTGGAGATAGCCCCTTGTGCTTATGTATTTTGTATAGTGAGTGCCTCAAGTTCACCCATGAGTTCAGCACAGAAGATGGCCCTTAAACTTGCTGTGACTGCAGATGTTATCTTGCAAAGCAGCTATCAGCAATGATGAGCAGAGACACACTGTCATTGCTGGGCTAGGATCAGGTGTCACGGAATTACGTATTCGGGTTTCCCTCATGGCTGAGATGATATTGAGGGAGGCATCCTATCATTTATTACCAAAAAATGACTAATAAACTGGTAACGAGCTCAATATGTTGCTACATAAATGTACAAAAATATTTTATGGTGGAAGCAGGCAAGAACTTGCTTAGAAAGTCCTTCTCTAGCTTGAAAGCTGATAAATACATATCTTTAGACGTTTTTAAAAAACATTTACTTAACTTGTAATTAATCAACAATTTAAGATGGTATAGATGCAAAGCTATTCAAATAGTTATCCAGTAGCTCCAGAAACATTTATTAATTTGCACTTTTTCACCATCTCTTTTATGTTATTTGTGGGTTGCGTAGACTGTACCACATTTTAAGAGTTAATTTCATCCATCAGTTTATTCATTCACCTAACAGGCTTTAACATGCCCATATGTACCAGGTGCTCACTGTGAGGGTGTGAAAAGGGAGGCAGAATAAAGTCACATAAAATCTGGGAGCTTGCCGTCCTGTCAGGAACCTAGGATATGTACATTAATAACTGCAACATGCATTAATTTGTGAAAACTGGCACTGAGAGGTAATACTCATGTTTTAAATTTGTGCATGCCATTTCTGTGCATGTTTATATTTGAGTCCGTAGCCCCGTGCTCAGAGCTGAGTGCTTGGGATTTGCAGGTGGGACAGGTTCCATGCCCCTGGCGGGCTCTGACTTCCATGCAGGGGAGAGTCAGGTTTCAGAGACCAATTTGCCTGGACGGTTGGCCACTTCACTGACACATTCCTCCCCTCCTGCTCCAG
Seq C2 exon
GGAAGCGGAGGTGCCGCTGGTGCTCCTGGAGAACGAGGCAGAACCGGTCCACTGGGAAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163359-COL6A3:NM_004369:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(32.8=100)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)