HsaINT0039397 @ hg19
Intron Retention
Gene
ENSG00000080573 | COL5A3
Description
collagen, type V, alpha 3 [Source:HGNC Symbol;Acc:14864]
Coordinates
chr19:10112444-10114390:-
Coord C1 exon
chr19:10114241-10114390
Coord A exon
chr19:10112558-10114240
Coord C2 exon
chr19:10112444-10112557
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-COL5A3:NM_015719:6
Average complexity
IR-S
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
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)