HsaINT0039572 @ hg38
Intron Retention
Gene
ENSG00000172752 | COL6A5
Description
collagen type VI alpha 5 chain [Source:HGNC Symbol;Acc:HGNC:26674]
Coordinates
chr3:130468795-130470967:+
Coord C1 exon
chr3:130468795-130469481
Coord A exon
chr3:130469482-130470870
Coord C2 exon
chr3:130470871-130470967
Length
1389 bp
Sequences
Splice sites
5' ss Seq
GACGTAAGT
5' ss Score
10.93
3' ss Seq
CCAGCCCACTCTCTCTCCAGGTG
3' ss Score
11.63
Exon sequences
Seq C1 exon
GACATGAAAATTATGGCAGAAAAGAAGAACCAGATCATACTTATGAACCTGGAGATGTCTCTCTTCAAGAATATTACATGGATGTGGCTTTCCTCATAGATGCTTCCCAAAGAGTAGGAAGTGATGAGTTTAAGGAAGTAAAAGCTTTTATAACCTCAGTGCTTGATTACTTTCACATTGCCCCCACTCCACTGACCTCCACCTTAGGAGACAGGGTTGCTGTCCTGAGCTACTCTCCTCCAGGCTATATGCCTAACACTGAAGAATGCCCTGTCTACCTGGAATTTGATTTGGTTACTTATAACAGTATACACCAAATGAAACATCATCTCCAAGACTCTCAACAGCTCAATGGAGATGTTTTTATTGGCCATGCCTTGCAGTGGACAATTGACAATGTCTTTGTAGGAACCCCCAATCTGAGGAAAAACAAAGTTATCTTTGTAATATCTGCTGGCGAAACCAACTCTTTAGACAAAGACGTCTTAAGGAATGTGTCTCTGAGAGCCAAGTGTCAAGGCTACTCCATATTTGTGTTTTCCTTTGGCCCTAAACACAATGACAAAGAATTAGAAGAATTAGCCAGCCACCCTCTGGATCATCACTTGGTCCAACTTGGCCGAACCCACAAGCCAGATTGGAACTATATCATCAAGTTTGTCAAGCCATTTGTCCATTTAATCAGAC
Seq A exon
GTAAGTCATTAATTCTCTTTGATTGCTTTTGCAATAGATTTAATGTTTCTGTGTACAGTCCATCAGCAGACTTAGTAAAATGATCCTCACTTCAGTTAAGAGTGGTAGAGTATAAGTGAGTAGGAGGCAGTAAAAAATCTCAGAGAAAATTCCCAGATTTTTTGACCATGAGCCTTGCTGCTGTGCTGCCAAAGTTTTAGCCAGGAAATCCTCAAATGGATGAAAAGTGCCCTTTAGCCCTAACCCGTGAGTGTTTACTATGTGGCAGGTTCTTTAAATTGATTGTGTCATTTAATCTTCAGTGCAGTCCTCAGAGGAAAGTATTCATAACCCCATTTTGCAAGTGAAAAGACTGAGATTCAGAAATGTTAAATAAAGTGCTTAAAATCTCACAAGTAATAATTAGTAAATTCTAGACTCAACCCCTCACATTCTGACCCCAGGGCTATGCTGTTGTCTAGTAAATCACACTTTAATTACTAAACCCTTAGCAAGGTGTAATGGTGTAATAAATAATATCACACTGACACTGCCCTCCACCTACTCCAAGGACTTCTATTTTGTCTTGTCATTATAAATTAACCTAAGTTCTGACTTGAATTCTTATGAGCCATAGGGACAAATCTCCTCTACAGCCTCTATGCCAGACAGCTGGTAGGGATTTTTTAGGGTGTCTTTACACAGTGGGGCTTTAAGGGTGGCTGCCCCAGCCTCTGCCCATGTGTTATGACTTTAGACATGCATATAGCAGCACATCCAAAACCTTGTAAGATCAAACAAGTCCTAGCGTGTGCTGGGAATTAGGAATGTGGCAGAGGCTACTTTGAATGGTCTCTGCAGCTCCTGTAAACTTACTAGAGAATCACAAGGTTGCAGGTTTTCTGGCATGCATAAAGCCCCAGGGCTTACACAGTTCGCAGGAATCTTGGAATTTAGCAGTTATGTTTAGTAGCAAGTAAAAATGTGCCTTCTCCCAACCCGAAGATAAGTAGGGCAGACAATTTCAATAGCTAATAGAGTCTTCTCCCAGAACTTAAAGTATAATTAAAAAAAAAATAAAATATAAACATTTTTTAAAAAATAGTCTTCTAGAAAGATCCTCCTTTTATAGAGAGAGAAAGAAATGATAGAAAGAATTTAGAGATGTCCTTAAAGTATATCACAAATTTGTGATAGAGCATTGGAATTATTTATTCAATGACTGGCTGTATCTTCTTGACTTTGCCAAGAACAAAGAATTTCCATGTCAGAGTGTGCCTATTTTGTGAAGTCCGTTATAAAAGTTGTTCTTGAAAACACTGCCAACCACGTGAAAACATGATCTGACTTTGGGTGAGATAATAATGTAGGTGGGTAAAATTTAGACTAACCAGCCCACTCTCTCTCCAG
Seq C2 exon
GTGCCATCAACAAATATCCCACCGAAGATATGAAAGCCACATGTGTTAACATGACCTCTCCCAACCCAGAGAACGGTGGCACAGAAAACACTGTATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000172752:ENST00000312481:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.096 A=NA C2=0.509
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=80.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAACCCCCAATCTGAGGAA
R:
TGGGTTGGGAGAGGTCATGTT
Band lengths:
349-1738
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains