HsaINT0039387 @ hg38
Intron Retention
Gene
ENSG00000080573 | COL5A3
Description
collagen type V alpha 3 chain [Source:HGNC Symbol;Acc:HGNC:14864]
Coordinates
chr19:9972919-9973623:-
Coord C1 exon
chr19:9973570-9973623
Coord A exon
chr19:9973027-9973569
Coord C2 exon
chr19:9972919-9973026
Length
543 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TCTGACCTCTTTCTGTAAAGGGG
3' ss Score
6.24
Exon sequences
Seq C1 exon
GGTGAGCGAGGGGACGCTGGAGACCCAGGGCCTCCAGGAGCCCCAGGCATCCCG
Seq A exon
GTGAGTGACTGTGTGATGTGGTCCCTGCACCCAACTCAGGGAACCCCTGACCCCTGGGCATCTTGGGCCACTTTGACCTCTGGACAGTGCAAGATCATCCACTCACCCCTGTCCTGTGGCCGTCCCTGATTACCTTGAGGAAGGACACCTGGAAGTTCTCAGATAGGGCTGCTATGTACAGTTCTGCAGGTTGCACACTACACAAGACTACATGACCCAGGGGATAGGTGAGGGCTCAAATCTGAGTCATGAGTCCTGACCTGAGGATGAGTTGCCCAGATGGGGCCCCTCTTCTAATTCACTCAAGGGCAGCACATGGGCTAGGCCAACCTTGCACATGACCAATGGGCACCTAGACCATCCAGACCTTTCACTGTCTTAAGTCCTAGCTCCTTCTGACCTTTGACCCTTGGACAACCTAGGCTACTCTGAACCCTGACCCCAGAAAAGTCCCAGACCACCCCAATGCCTGAATCCAAGTATGCTAATCCTTGATCCCTGGAGAGTCCAGGCCACTCTGACCTCTGACCTCTTTCTGTAAAG
Seq C2 exon
GGGCCCAAGGGAGACATTGGTGAAAAGGGGGACTCAGGCCCATCTGGAGCTGCTGGACCCCCAGGCAAGAAAGGTCCCCCTGGAGAGGATGGAGCCAAAGGGAGCGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080573:ENST00000264828:50
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(19.0=83.3),PF0139113=Collagen=FE(27.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(56.5=100),PF139001=GVQW=PU(2.3=2.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
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