HsaINT0039568 @ hg38
Intron Retention
Gene
ENSG00000172752 | COL6A5
Description
collagen type VI alpha 5 chain [Source:HGNC Symbol;Acc:HGNC:26674]
Coordinates
chr3:130439522-130440825:+
Coord C1 exon
chr3:130439522-130439615
Coord A exon
chr3:130439616-130440165
Coord C2 exon
chr3:130440166-130440825
Length
550 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
GTCTCTCTGTGTGTTTTCAGATA
3' ss Score
11.85
Exon sequences
Seq C1 exon
TTTGACAACACTGGAACATTTCAGGTGATTCCAGTTCCTCCAAATGGGGAAAATCAAACATTAGAAAGACTTCGGCGCTGTGCACTTTGCTATG
Seq A exon
GTAAGACCAATGAAGAGAATTGACTGTGCTGAAGAGCTTAAATGCCTTCTAGATGAGTTATTGAATGTGGTTTTATCCAGAGATTTCTATTTTTAATCATAGGTTCTATTTTCAGTTTTCTAGTTTTTCAATACCATATGTCATGGTTTCAATCTCTGGAATGTTTGGAGTTTCCATAGAATGTGAAAATTGGTTTAGAAAATTATCCCAACCAATGTAGCATTTCTTGGGGACAATTGGGTAGTTTGTATCAGAAGTCTCTAAAATATCAAAAATATTTCCTAAATGAGCTTGGACATGACTTGTACACTGCAGGTATCTGTGCTACCTACATCTGCTTTCAACAAAGCCCTTCCCTTATTGTCTGCTAGTGCCCGGAGAAGTACCGGGACATTGAAAATTTCTCATTAATTTAAATTATGTGAGATCAAAGAGATATTGATCAAATTATAATTCTTGGTAATTAGTCACTGAGTCACTTGAAGATCTCAAACAAGTGTCTTGTTGGGTCAGTGTTGAACCAATGATGTGTCTCTCTGTGTGTTTTCAG
Seq C2 exon
ATAAATGTTTTCCAAATGCTTGCATTCGAGAGGCTTTCTTACCTGAAGATTCATACATGGATGTAGTCTTCCTCATAGACAATTCTCGGAATATAGCAAAGGATGAGTTTAAGGCTGTGAAAGCCTTGGTGAGCTCAGTGATTGACAACTTCAACATTGCTTCAGACCCTTTAATCTCAGACTCTGGTGATAGGATTGCTTTGTTGAGCTATTCTCCTTGGGAAAGTTCCAGGAGAAAGATGGGTACAGTAAAAACAGAGTTTGATTTCATCACTTATGACAACCAACTCCTAATGAAGAATCACATCCAGACTTCCTTCCAACAGCTAAATGGAGAAGCAACAATTGGTCGTGCCCTACTGTGGACCACTGAAAATCTTTTTCCAGAAACACCCTATCTAAGAAAACACAAGGTCATCTTTGTGGTCTCAGCTGGAGAAAATTATGAGAGAAAAGAATTTGTAAAAATGATGGCTTTGAGGGCTAAGTGTCAAGGCTACGTCATATTTGTGATTTCTCTGGGCTCTACACGTAAGGATGACATGGAGGAGTTAGCCAGCTACCCACTTGATCAACACCTGATACAGCTTGGGAGAATACATAAACCAGATCTGAATTATATTGCGAAGTTCTTAAAGCCATTTTTATACTCGGTCAGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000172752:ENST00000312481:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.062 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(3.1=15.6)
A:
NA
C2:
PF0009223=VWA=WD(100=81.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGCTGTGCACTTTGCTATG
R:
GCTGTTGGAAGGAAGTCTGGA
Band lengths:
347-897
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains