HsaALTA1054065-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000197467 | COL13A1
Description
collagen type XIII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2190]
Coordinates
chr10:69878039-69880553:+
Coord C1 exon
chr10:69878039-69878065
Coord A exon
chr10:69880414-69880502
Coord C2 exon
chr10:69880503-69880553
Length
89 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TGCTCCTGGCCCCCTGCCAGCTC
3' ss Score
5.49
Exon sequences
Seq C1 exon
GGAGTAAAGGGCCAACCAGGCGAGAAG
Seq A exon
CTCCTTCCCTTTGGTTCCTCTCTTTCCCGCTCCTCTTCTCCATACCTCCCTGCCCCTCGCTCCCTCTCCCCCTTCCTCTCTCCCCGCAG
Seq C2 exon
GGGTCCCCCGGAGACGCTGGGCTGTCCATCATTGGTCCCCGCGGCCCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197467-9-15,9-14-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(15.4=100)
A:
NA
C2:
PF0139113=Collagen=PD(17.4=47.1),PF0139113=Collagen=PU(9.8=35.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGTAAAGGGCCAACCAGG
R:
TGGACAGCCCAGCGTCTC
Band lengths:
55-144
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains