HsaINT0039397 @ hg38
Intron Retention
Gene
ENSG00000080573 | COL5A3
Description
collagen type V alpha 3 chain [Source:HGNC Symbol;Acc:HGNC:14864]
Coordinates
chr19:10001768-10003714:-
Coord C1 exon
chr19:10003565-10003714
Coord A exon
chr19:10001882-10003564
Coord C2 exon
chr19:10001768-10001881
Length
1683 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TCCCTCCATCCCTGCTCCAGACC
3' ss Score
8.41
Exon sequences
Seq C1 exon
GCTCCCCAGGGTGAACCAGAAACCCCTCGTCCTCGGCGGAAGGGGAAGGGAAAAGGGAGGAAGAAAGGGCGAGGTCGCAAGGGGAAGGGCAGGAAAAAGAACAAGGAAATTTGGACCTCAAGTCCACCTCCTGACTCCGCAGAGAACCAG
Seq A exon
GTAAGGGCCCTGAGACCTCTCACTTCCGGTTTTGACCACCTGACTTCCGGTCTTGACTGTCTGACTTCTGGTCTTGGTGCTTGACTTCTAGTCTCCCATCTCTACTAATCTCTGGTCCCTCATCTATGATCTTTTTCTCTGGTCTCGGATCCATGAGCTCTGACTTCTCTCAGCTGACTGATGACTGTCAGGGTGACTGATAACAGGGTGGGGGTGGGTCCCATCTTATGATCTCTCCCATCTCTGACCCCCTCAATCTCCAGTCCTGGGGCACTAGAGGGAGGGGACAGACCCAGATAAGTTCCTGATTTTAAGGGAGTTCTTGATGAGGGCTACTGTTTAAGGGGGGATCATTGGCTGGGTTGAATGACGTGTTCATTAGTTAGTGTGTCATTGTTTGGGGTTCCCTGCTTGGGGTCACTGGGGACAGTTATTCATTGGGAGAGTCATTAATTGGGGGCATTATTTGGCTTCCCTGATAGGGATTGCTGGATAGTGGGGAATCATTGAGGGAGATATTAATTGAGGTCAGTGTTTGGGCTGCACCTAGCTGGGGATCACAGTGGAAGGTCATGGATAGAAACCATTATTGGTGTTACTGATGTCCCTAGTTTGGGGTCAATGACTGGGGGGTTGTTGGTGGGTGGTCACTGACTGGAAGTCATAGTGGGGTCACTCATTGGGGCCACAAGTTGGAAGAGTGATTTTCAGGGGGTCGCAGATGGGGTAATTGGTTTGGGAGTCCCTGAGGGAATTATTAGTTAGGAAGTCATTGATGGGTGGAATTACTATTTGGGGGTCATTGGTTAGGACGCTTTTGTTGCGCTCATTTATGGGTATTCACTGTTGGAGCATCACTGGTTAGAGGAATAATTGATTAGGGGTCACCGATGGGGGTTATTAGTTGGAGAGTCACTAGTTAGTGCTAATAGCCAAGAGATGTCACTGGTTGAGGTCACTGGTTAGGAAAATCACTGAATGGAGCAGTAACAGGTTGAGGCCATTGATGGGAGTGGGAGGGGTTGTTTGTGGGTCTCTGGTTCTAGAATCACTGGGGTCTGTTGATGTAGGTCATTCTTGGTGGGTCACTGGGTTGGGGGGTCCTTGGTGGGGGTCATTGCTTGGGGTCTTTGGCTGGTGGGGGAGTCACTGGTTGCACTACATCTCAGTTCCAGATCTTCTTGGCCAAGAATACAAACACCAGGAGTAGTGGGCCCCTCTTCAGCCCCTTCCTCAGCCTTGTCCCCTCACCTGGGACCCCACCACCCTCTTCCCACACCCCCCCAACCCCCACCTTGACCCAGTTCCTCTGCAGCTGTCCAGGCCAGAAGGAGCCGCCACTCCCTCTCTGACTGTGGCCTGCTGGCCGCTGAACTCTGCCTTGGGAGAGGACATGTGGGCTAGGCTTCCGGGAGCCTGGCCCTGAATGTTGGACCTTGACCTTGACCACTGGGCTTCAGGGCCAGCCTGACTCAGCACCTCCTCCATCCACGGTGGCTCCCTCTGCTGGCAGCCCTGGTCCAGCTGGCACACTTTTGTCTCCATTGGCCTCTGGTGCTCTTTGGGGAGCCTCCTCTGTCCCTGTCCCCGGACTGGGAGCTCCTGGGGACAGTGGGAGGGTGCCTCCCTTTTGTCTTGATTGCCCTCACCCGAGACCCAAGGCTCCCTCCATCCCTGCTCCAG
Seq C2 exon
ACCTCCACTGACATCCCCAAGACAGAGACTCCAGCTCCAAATCTGCCTCCGACCCCCACGCCTTTGGTCGTCACCTCCACTGTGACTACTGGACTCAATGCCACGATCCTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080573:ENST00000264828:6
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCCCAGGGTGAACCAGAAA
R:
TCTAGGATCGTGGCATTGAGTC
Band lengths:
262-1945
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