HsaINT0039212 @ hg38
Intron Retention
Gene
ENSG00000197565 | COL4A6
Description
collagen type IV alpha 6 chain [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chrX:108164600-108165038:-
Coord C1 exon
chrX:108164877-108165038
Coord A exon
chrX:108164699-108164876
Coord C2 exon
chrX:108164600-108164698
Length
178 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGG
5' ss Score
10.26
3' ss Seq
CTTCCTTTGGGCTTTGTCAGGCA
3' ss Score
5.74
Exon sequences
Seq C1 exon
GCCGCCCAGGCCCCGCTGGACCCCCAGGTCCCCCTGGGCCATCCTCGAATCAAGGCGACACCGGAGACCCTGGCTTCCCTGGAATTCCTGGACCTAAAGGGCCTAAGGGAGACCAAGGAATTCCAGGTTTTTCTGGCCTCCCTGGAGAGCTAGGACTGAAAG
Seq A exon
GTACGGCTGCTCGGCTGGCTGCTGGGCCCTTCCCCACTCCACGGCCAGGACTCCTTCCTGCAGTCCTGTGAAGAGAGGCCGGTGGCTGATGTTCTTCCCTACCTCACCCCTGCCTATCCTCCACCCCTACCACCCCTACCATGCCGGGACCTGACTTGCTTCCTTTGGGCTTTGTCAG
Seq C2 exon
GCATGAGAGGTGAGCCTGGCTTCATGGGGACTCCAGGCAAGGTTGGGCCACCTGGAGACCCAGGATTTCCCGGAATGAAGGGGAAGGCAGGGCCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197565:ENST00000372216:39
Average complexity
IR
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=PD(71.0=80.0),PF0139113=Collagen=PU(23.8=27.3)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(52.4=100)
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:
TCCCCCTGGGCCATCCTC
R:
CCCTGCCTTCCCCTTCATTC
Band lengths:
226-404
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