HsaINT0039560 @ hg38
Intron Retention
Gene
ENSG00000172752 | COL6A5
Description
collagen type VI alpha 5 chain [Source:HGNC Symbol;Acc:HGNC:26674]
Coordinates
chr3:130421325-130422782:+
Coord C1 exon
chr3:130421325-130421360
Coord A exon
chr3:130421361-130422719
Coord C2 exon
chr3:130422720-130422782
Length
1359 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTG
5' ss Score
7.76
3' ss Seq
TTTTATATCTGAATCTTCAGGGT
3' ss Score
8.22
Exon sequences
Seq C1 exon
GGCCCAAGAGGATTCCCTGGAGATGCGGGGCAGAAG
Seq A exon
GTATTGTATGCATGACCTTTTGAAATTACCATGATCTTAACCTTCTACTTGAGAACTGAGATAAACCTGTAGGTCTGAATGAAATGGGGACAATAAGGAGAAACCAAGGACAGTTGTTTTCCTTGGGCTTCCTGAGGAAAGAATCATATTTAACCCCTGTGAATCTTTACATTGGAAAAGATTGTTCTGTCCATCATTGCCTGATGCCTCTGCCTTGAAAGCCTACCTCCAGGTATCCTCTCAAGTTCAGTCTTCTGTTCTCTTCTTGATTTTCTGCCTTGGTGATTTCATTCAATACTCTTGGCTTTGGTTATTGCTATTTGTTCTTCATTATTGTGCCCTTTATTTTCTCTCACCTGAAAGATTACAATATCCTTCTAATTGGGTTCCTCCTTCCATCTTTTCCCTGATTCAGTTAATTCCAAACACTACTGTCACTTGATTTTTTTCCAAAGCATAGCTAAATTATGCCACTTTCCTACTCAAACATCTTCAAGAATTCCTCATTGCCTGCCAGATAGAAATCCATCTTCATGCTGTAGGAACAGACATACCTTTCATCTCAACCCAAGTAGCTTAAGTTATGTCTGTTTTATACATTGGAATTCTGTAAAAAGATCTCCCTTAGAAAAAAAAGTCCAGAACAATGTCTTCTACATAAGTGATGCTTATATTAAAATACAAAATATGGGTTAAAAAGTAGAATATCTAATTAATCAAATAAAGTATAGGAAAACTGTCAACTGCTGAATCCTCTTAAAACTATTTTTAATGAATGAATTACCAAAAGAGATTCTTAAGTACAAAAGGGTGCAAAAGGGACAATATAAATCACCATTAGAAAGAAAGTCCTCATTGTAGAGGATCAATTTTCCAATTTACTGATAAAGGGAGAAAATTAGCATAATTCAACTTACTGATAAATGTGAAATAAGCATGTCGATAAATAACTGTCAAAATTTTAAAAAATCAGAATAGATTATTTTCACCTCAACTTTTTTCATAAATGTTTTATGAATTTATAAAGTAATTCATTATTTATTTCATATAGTCAATACTCCAAATGTTTTTCTGGGTTTTCAAGCATTTTCTTTGGATATTCGTAGTAACTGGATGACCACTGAATTGAAATGTATATGTAAATATTTATATTATTAAAAAATTAAAAATAGTTTGAAGAATAAGTGTACCAATGACTTAGTTCCAAATGACAGGAAAAGATGACATTTAATGTTGTATTGGCCTTCATTAATGTATGATTGTCATAATATCAATCAAGTTTGAGTCCAGAGAGTTTTTTTTTTAATTCTTTCATAGCAAATACTTTAACATCTTGACTTTTTATATCTGAATCTTCAG
Seq C2 exon
GGTGATATTGGTAATCCTGGAATTCCTGGGGGACCTGGACCCAAAGGATTTAGGGGACTAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000172752:ENST00000312481:27
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(12.8=100),PF0139113=Collagen=PU(8.5=41.7)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=100),PF0139113=Collagen=FE(33.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
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