HsaINT0039388 @ hg38
Intron Retention
Gene
ENSG00000080573 | COL5A3
Description
collagen type V alpha 3 chain [Source:HGNC Symbol;Acc:HGNC:14864]
Coordinates
chr19:9971205-9973026:-
Coord C1 exon
chr19:9972919-9973026
Coord A exon
chr19:9971259-9972918
Coord C2 exon
chr19:9971205-9971258
Length
1660 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTAATCATTCTGTGTTCCAGGGC
3' ss Score
9.78
Exon sequences
Seq C1 exon
GGGCCCAAGGGAGACATTGGTGAAAAGGGGGACTCAGGCCCATCTGGAGCTGCTGGACCCCCAGGCAAGAAAGGTCCCCCTGGAGAGGATGGAGCCAAAGGGAGCGTG
Seq A exon
GTGAGTCCTGGGGGGAAGTGGGGGCAGACATGGGAGGGGGCACTTGAATGTACTTGAAGCTCTCCCAAACTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTCACCAGGCTGGAGTGCAGTGGCACGATCTCAGCTCACTGCAACCTCCGTCTTCCGGGTTCAAGCGATTCTTCTGCCTCAGCCTCCCAAGTAGCCAGGACTACAGGCACGCGCCACCACACCCAGCTAATTTTTGTATTTTTAGTAGAGATGGGTGTTCACTATGTTGGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCAGCATGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCGCTCGGCCAAAACTCTCCCAGACTTCTAGCCAGGGATTGCATCCTCTAATTTACTGATCTCATGAGTAACCCCCAGAACACGGATGAATGAATGAATGGGTGGATGGATGGATTAATGAATGAGTGGATGAATGTATGAATGAGTGAATTAATGAATGGACAAGTGAATAACTCAGTGGATGGATGAATACGTGAATGAATAAATGGATGAATAAATGAGTGAATGGATGAACGAGTGAGTGAATGGATGAACGAGTGAATGAATGGATGAACGAGGGAATGAATGGGTGAATGAGTGAATTAATGGAAAAATGAATAAATCAGTGGATATATGAATATGTGAATGAATAAATGTGCACGAATAAATGAGTGAATGAATGGATGAATGAGTAAATTAATGGATGAATAAGTAAATTAATGGATGCATGAATATGAATGAATGGATGAATGAATGAGTGGCCGAATGGACAAATGAGTGAGTGAATGAGTGAATGGATGCATGAATGAATGGACAGAGGCGCAAGTGAACAAAATGACTGAAGAGATGAGTGAATAAACGAATGGATGGATGGATGAGTGAATTAGTGAGTAAATGTGTGAATGAAACATAAACGTGCAGTGGTTATACATCATTGAATGGCAAGAAAGTTGATTTCATGGCAGATCATTCTAACACTTGAATTAGTGAGTAAATGTGTGAATGAAACATAAACGTGCAGTGGTTATACATCATTGAATGGCAAGAAAGTTGATTTCACGGCAGATCATTCTAACACTGTTGCAAAGATTAAGGTTGAATTGGGTCAGATTTGGGGTGGATGTGGGATTTGGCTTTGAGGTGAAGGTTGAGGCCCTTCTGTCACCACAGTAGAGGTTGGGGCGGGTGGAGGTCAGGAAGGGGCTTTAGCATCTGTGGGACCTCGACTTGAATGGCATTGTTTGGCGTGTCCCTTCTCTGAGTGTATGAATGAATGGATGGATGGATGAATGAATGAATGAATGAGTGAATGAATGAATAGACGAATCAATGAATGAATAGACAAATGAATGGCCAGTTTTCTCTGTGAGTCCCGAGCTGAGAGGCTGTGAGGACGCTGCAGTGAGACCATGCGTGCGGCATTCTTAGCTCAGCGTCTGCACCCATGAAACACGAGAATGTTCGCTCTACCAAGCCAGGGATTTTATGTTTTGTTCACTAATGTGTCCCCAGAAACCAAACTGTTCCTGGATACAGTTGATCTGTTCCATAAATGCATGATTGCTCCACAATTCAGAGATGTGATTATTAATCATTCTGTGTTCCAG
Seq C2 exon
GGCCCCACGGGGCTGCCCGGAGATCTAGGGCCCCCAGGAGACCCTGGAGTTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080573:ENST00000264828:51
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=FE(56.5=100),PF139001=GVQW=PU(2.3=2.8)
A:
NA
C2:
PF139001=GVQW=PD(18.6=80.0)
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