HsaINT0039245 @ hg38
Intron Retention
Gene
ENSG00000130635 | COL5A1
Description
collagen type V alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr9:134782667-134785096:+
Coord C1 exon
chr9:134782667-134782720
Coord A exon
chr9:134782721-134784988
Coord C2 exon
chr9:134784989-134785096
Length
2268 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGC
5' ss Score
8.19
3' ss Seq
TCCTCTTTTCTGGCTTGCAGGGG
3' ss Score
10.27
Exon sequences
Seq C1 exon
GGTGAAGACGGCTTTCCTGGGTTTAAAGGAGACATGGGCATCAAGGGTGATCGG
Seq A exon
GTGAGCATCTCAGGTTTGGGATTTGGGCTGGGGAAAGCTGGGTGGGCTTGGCCGTGTGGGAGGGGGTGGGGATGTTTGCCGCCACAGGGCAGCTTCTCAGAATGGAGGTAAACTCTTGGTAGAGATTCCTGGTGGGAAGGGGACAGTGGCGTGGAGCCCAGGGCCCGACTCTCTCCAGCTCCTCTTCACCTCCTCTTCCTCAGTTTGCCCCTTGGGGACTGGGAATAACCTGTGGTCGCCAGCTCCTCCGCCCAGTGTCCCACACAGGGGGTCAGTGGGGCTGGGTTCACTTCTGACTGCACCTGTGGACTGCAGAGTTACTCACCTGACTCAAGAGGGATAAGCGGTGCCTGGGAAGAGAAAAGAGAGCAGCTACGGAAATGACCCAGCCTACCGAAGGAGCGCAGCTGCTGCCCAGGCCACACGGCCGGCGCCCACAGGGCAGCACGCGACGTGGGTCTAGGATCCCTGTGAGCCTGGGGAGCGTCCTGGTCCCCAGACAGTTCTTCAGGGTCCCTGGGACTCCCACACAGTCCTGTGGTCTGTGATTTTGGCTCAGGAGACCTGGCTTATTTTTAAATGAATAATTTAGCTCGGCTCCAGAGAAAGCCGGTGGGTGCTGGGAGGGACTGGGGCTTGCCGGCAACCACAGAAAGTGACGGGCTGCACGTTCCTGTAATTAAAGAGAAGGTGACGCAAAGGGCACGAAGGAAGGGTAGGGAGCTCTTAGAGCAGCCAGGGTGGCCAAAAGACTCTTGGAGGTTTCCCCAGTAACCTCTCAGCGAGCAGAAGCCCAGCAGAAGGAACCGAAGACGCCTCGGCCTCCGGTGGGCACAGCCGTGGTGACAGCTGTGCACGCACCGGGACGGACATCTGTCGGCTGCAGCAGGGCTGTCACCCAGCTGCCGCAGTCATCCCCCTGCAGCACCGGCTCGCAGGTGGCTTTCCAGAACAGGAAAGCCCCACACACTTGGCACTTCGTCCCAACCTGGCAGGCAAAAGGCAGAGGCAATCTGCACCTCTGTGGGAAGGAAGGGGGAGGAAGGAGGGGATCTCTTGCGCAATGTTGTCCCAGTTAAGTTGCTGCTAAAGGCACCCATTCTAGAACTTCTTTCCTAGTAGAAGGCTCCTGAATCCCCACATCCCAGCGGCTTCTCGGTTTGATGGTGAAAGTCCTTTTCTCCTCCTTTCTGATGCCTCTGTTCACACATGTGGCGTCCACGTGACGAGGGTGCAGCTTCAGAAGAGATGACACACGTTCCCGTGCCAGGGCTCCGAGAGTGGAGCTCTCGTTGCCATGGGACGAGGGTGGGATGCAGGGGTGGGACCCATCCTGAGCCCAGGGAACAGGACCCCATATGCGGACCTCTTCAGAGAGCACAGCCTGGCACTTTGCACCTTCTCGGTGCTCTGTAAATGTGTGCCGGGTTATTTTGTTGAACGAGAGGAACACCTCTTAGGGACAGAGAGTTCCTGACCCGATGACAGATTAGAGCCTCAGAATTAGGAAGTTATTCATTTTTCTCTATCTGAGCAATACACATTTCTGTTGTGGGCTTGCACCACTGCTTTACAGCTGCTCTTAGAGACAGATGATCAGAGGAGGATCCATCCATTGCTGGACAAAGAGTGCCGGGAAGGGCATTTAGAGACTCTGCCGTAGCGCTACCATTGCCTGGGCAGGCTCCAGAGCCCTCTCCCCTTTCTGAGCCCCGAGCTCCCAATCTGTAACTTGAGGAAGTTGGACGAGGCGGAATTTAAGCCCGTCTGTTCCTGGGACGCCTCCTGAGGCCCTCCCGTGTGCTCGTTATGCCCAGGTAACTGCCCCATCCGGGGCTGGGGTCCACTTCCATACCTCCTGGGGTTTCAGAAGCAGCAGCAGCTCCCAGTCACTCTGCTCTATTTGGAGAAACAGCAATTCAGAGCTACTATTGTTAACCAAAGTTATTTTAGCTAAGAGGCACTCAATTTAGAGAAGGTAATTGGGAAGTAGGAGCCTGCAGCCTTGAGAAAATAAATAGCAGGCAACCTCGGTGCAGAGACCAGCTTCCGCAGAGCCCGGGAGCCCGGGAATTCGCGGTACAATGCGCTCGCTTTGTCAGTGGCTCCGGGAGCAGCTCCGTGGTCTGAGTGAGGCCGAGCTGGTGGAGCAGCTCTGACCACAGGGTGCCTGTGACCTGTCCCCTTGCTCCTTGCTCTCAGAATGGTGGTGGAGAATAGTGTGTGTGCGGGGGGTGGTCTTCTCACCTCCTCTTTTCTGGCTTGCAG
Seq C2 exon
GGGGAGATCGGCCCACCCGGTCCCAGGGGAGAAGATGGCCCTGAAGGCCCAAAGGGTCGCGGAGGTCCCAATGGTGACCCCGGTCCTCTGGGACCCCCTGGGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130635:ENST00000371817:29
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(22.1=100),PF0139113=Collagen=PU(7.9=27.8)
A:
NA
C2:
PF0139113=Collagen=PD(9.1=19.4),PF0139113=Collagen=FE(55.6=100)
Main Inclusion Isoform:
NA
Other Inclusion 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