HsaINT0039254 @ hg38
Intron Retention
Gene
ENSG00000130635 | COL5A1
Description
collagen type V alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2209]
Coordinates
chr9:134798408-134802007:+
Coord C1 exon
chr9:134798408-134798461
Coord A exon
chr9:134798462-134801953
Coord C2 exon
chr9:134801954-134802007
Length
3492 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
CAGTGACTCTCTCTTCACAGGGT
3' ss Score
8.69
Exon sequences
Seq C1 exon
GGCCCTCCAGGCAAGGATGGACTCCCAGGACACCCTGGACAGAGAGGCGAGACT
Seq A exon
GTGAGTATCGAGGGTGCTGGGGGACGTGGCTGGCTGGCTCTCTGACCACCCTGCACGTGGGCACAGCCCTCGCTGCCCAGCGCCATCTAGGACCCTCCTGGCCTGGGAGAGACAGGTTGGCCTCAGAAAGGCTCCCAAGGGCCGGGCCGGCTTCCGCTGACTCAGAGCCAGGCTGTGAGGCAGGGCCAGGGCAGAGCAGTCATGCAGGCCGGCAGCGCCTTATGGCATCTGTGGGCAGAAGGCAGGTGTTGGCTTTGGGCTGGTTTTGGAAACTTTGGTGAGAGGCCACATTTAAAGACACACACAGATTATCCTGGGCCGACTGAAGCCTCATGCATCCAGCCTTATTTTCCCTCTAGAATAATGCTGAGTGCTACCCCGCTTGAGGGATACGTCTTTTAATTGAGAAAGTGCTGGGAAAGGGTCTACATGTTACTCAGCGTCATTCAGTCATTCGATGCTGCAATACTTCAAGAGGGCGGCTGTGGGCCATGCACCAACCCCACCCACGTTCACCCGGGCCCTTCCAGCTCCAATCCAGGGGGTCTGGAGGATGCCTGCAATGTCCCTTTTTACACTAAAGAAAACAAGCGCCAGTCAGGTGGAAGTGGCCTCTAACTAGTCACTCCGCTGGGCACATGGTCTTTGTAGTCAGAGACTCCCCTTTGACCTTGCCCTTCACTTTAGAAATGCATATCACAGGCTACTTCATCCAGACCAGAAAGGACTCCAGTGTTTTCAGTTGGGAGAAAAAGCCCTCATCAGAAATGGGATCATTTTCCTGGCCCCATCAGCCCTTCGAAATTTGGCCCAGCTCCCTAAAGGTGTGTTTCAGGAAAGGGTGCAGGCACGCCTGTAACCTGGCCCACACCTACAAGCTTGGGGCTCCAGGCTCTGAATATCTGGGGACGTGCAGTGTCGGGTGACTTCCTCGTCACCACGCTGTGTTCCTTCTCCGAGTGCCCACCTACTCTGTCCAGCTTAAAGGATGAATTGCACAGATGCAAACATTTCCCACAGAGGAGAGTGAGGGGCATGCCAGGATCACTGCAAGGGTCCCTGCAGCCAGGTTTCTAGGGATCAAGGTCTCTACAGGACTCTCCCAGCAAAAGCAGGTCCCCTCGTGGAATGGGTCTCTGAGTGCCCTGTTGAATATATTCTCCATGCCTGCTTTGAAAAAATCCCCTTTGTCTCTCTTTGGTTCATCGTGATGAAACCTCTTTTAATTATACCTTCACTGGTGTTCTGCACGGCGCATGCTGCCTGATAAATGGAGATTGCTTTGCTCTTTTGTTTATAGAGAAAAATTAAAACATTTCTTCTGAGCTTTGCATATTTTTCTCTAATGCCTTTTCAAGGAGACAAGATAGAAGGTTTTACATATTATGTGCTTTTCTCCCTCTGACTTATTCTGGACGGAGGCTGGTGAAAGAATTAAGCTGCTTGTCTCTGCTCAGAAAGTTGCACATGTACTTCCGGCTGCCTTCTGCCACCCCGGCCACCTCTCTAGACACATGGCGCTGGAGTGATGCCTGTGTCTCTGAGAGCCACTTGGGACATAGCATCTCCTCCATGGGCTAGTCCAGACAAGCCTTCCAGAAAGAGCTTCTCTGCAGTGTTGATTTCCTTCTTTTTTAAAAATATGAAACACCAACGGTCATTATTTCTCCTAAATGTGAGCCAGAAACTTATTTCTCAGCAAAGGGCTAAGGTCATATTCTGTCCTCAACAGCCAGGGTGGCCGAGGGCCCTGGGGAGGCCTTTTTTGTTTCGTGTTAACTTTGACATTAGCAAAACTTAACCAAGGCTCCGATCTCCCTTCAGGCTCTTGAGCTCTTCTCCCCGGGTCCACTGAGCAGGGCATGCCCTTGACACCCATCCACCGTTCCTTACTTCTGACCCCATAAGTGCAATGAACATTAGAAACGATCATTCTAGCCCACAGCTGAGCTGGGCTTAAAGAGGCGAGCCCTCCTAGAGTTTGCAAAGAAGCTAAGTCTGGGCTGGGCACAGTGGCTCACGCCTGCAATCCCAACACTTTGGGAGGCCGAGATGGGCGGATCACCTGAGGTCGGGAGTTTGAGACCAGCCCGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGCAGGCACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAATCCGGGAGGTGGAGGCTGCCGTGAGCCGAGATCGTGCCATTGCACTCCAGCCTGGGCAACAGGAGTGAAACTCTGTCTCAAACAAAAAAAAAAAAAAAAAAAAAAAAGAAGCTAGTCTGCTGTGGGTTCATGTGGCCCCGTGGCTTGGTGTGAGGTTTTGCCTCTGACTGCTGGACAGTGAGTCAGTGAGCCCAGGCCTGAGGCCGCTCACCCTCCAGCCCTAGCTTGGCCTCAGGGCCAGCCACCTTCTCCTCCAGCGTCTAGAGTTTGCCTCGAGGCCTCCGGGTAGAAGGTGTGCATGTCTCCACCAGTGTCATGTGGCACCTGCAGATGGCTTCTCGCTGGCACCTGTCATGCTCTGCAGACGTGCCTGGAAAAGAAGCTTATGTTGCCTTAAGGTCATCTTTCTCCTTTGAGGGAGAGTACAGAAGTCGTGGCGACACCCACAGCCAAGCCAGGATCGTTATCTACGCGTGAGCATGCAGAGCGGGCGTGAGATATTCCCGCTGAATCAAGCTAAAAATAACGCATCCAAGCTGCCGAGTTATGAAAGCAGCTGGCCCTCGCTCTTGCCTGTTTTAAATACATGCTGAGGAGCACGCGGGCAGAGTCACCCGTCGTGCATCAGAGGCGTTCACGCCAAAGCAGGTCAGTCGTCACAGAGCCACTGCTGAGAAACAGCCAGAGGTAGTCGCGGGTCCAGAAAGGGCACCAAGCCAACTCAGAAAAGGAGCGTTTGGTGACATGATAAAGGCGAATCGCGTCGGCCTAAAGATGCAGAGGCAGGAGAGCAGCCAGTGAGATGAGCTTGTGTGGCTTCGTTACCCTCGTGAAATTAGTGCAAACGCACGGTGGCTCACGCCTGTAATCCCCGCACTTTGGGAGGCTGAGGCAGGTGGATCACGAGGTCAGGAGTTCGAGGCCAGCCTGACCAACATGGTGAAATCCTGTCTCTACTAAAAATACAAAAATTTGCCAGGTGTGATGGTGTGTGCCTGTAATCCCAGCTACCCAGGAGGGTGAGGCAGGAGAATCACTTGAACCTGGGAGGCAGAGGTTGCAGTGACCCAAGATCGAGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCTCCATCTGAAAAAAAAAAAAATGAAACAAGAGACATGGGCCTCTTACACAAAGTCTGGAACATCTACTCTGGGGGGAAGGGAGGTGGGGGGCAAGCGTCCTGCTGAGAACAGTGCAGGGCAGGGTGGCGCAGGCCACTGCAGCACCGTCAGTGCAGTGACTCTCTCTTCACAG
Seq C2 exon
GGTTTCCAAGGCAAGACCGGCCCTCCAGGCCCCCCCGGCGTGGTCGGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130635:ENST00000371817:37
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(21.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.5=100),PF0139113=Collagen=PU(25.8=94.4)
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
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development