HsaINT0039511 @ hg38
Intron Retention
Gene
ENSG00000163359 | COL6A3
Description
collagen type VI alpha 3 chain [Source:HGNC Symbol;Acc:HGNC:2213]
Coordinates
chr2:237371732-237375020:-
Coord C1 exon
chr2:237374412-237375020
Coord A exon
chr2:237372338-237374411
Coord C2 exon
chr2:237371732-237372337
Length
2074 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGC
5' ss Score
10.12
3' ss Seq
TGCTCACATTTGTTTCGCAGGTG
3' ss Score
9.42
Exon sequences
Seq C1 exon
TTTCAGGTGAAAAGGACGTGGTGTTTCTGCTTGATGGCTCTGAGGGCGTCAGGAGCGGCTTCCCTCTGTTGAAAGAGTTTGTCCAGAGAGTGGTGGAAAGCCTGGATGTGGGCCAGGACCGGGTCCGCGTGGCCGTGGTGCAGTACAGCGACCGGACCAGGCCCGAGTTCTACCTGAATTCATACATGAACAAGCAGGACGTCGTCAACGCTGTCCGCCAGCTGACCCTGCTGGGAGGGCCGACCCCCAACACCGGGGCCGCCCTGGAGTTTGTCCTGAGGAACATCCTGGTCAGCTCTGCGGGAAGCAGGATAACAGAAGGTGTGCCCCAGCTGCTGATCGTCCTCACGGCCGACAGGTCTGGGGATGATGTGCGGAACCCCTCCGTGGTCGTGAAGAGGGGTGGGGCTGTGCCCATTGGCATTGGCATCGGGAACGCTGACATCACAGAGATGCAGACCATCTCCTTCATCCCGGACTTTGCCGTGGCCATTCCCACCTTTCGCCAGCTGGGGACCGTCCAACAGGTCATCTCTGAGAGGGTGACCCAGCTCACCCGCGAGGAGCTGAGCAGGCTGCAGCCGGTGTTGCAGCCTCTACCGAGCCCAG
Seq A exon
GTACGCAGGGAACTCTTTGCATCCTCACTCAGTGTCATTGTCTGGGGCTACTTGTCTGGACTGTGGGCCACAAGGTGTTCTCAATTTTGCTTTTCCTGCCATGTGAAGTGAAAACTAAAATTACAGGAAAATTTAGGAACCCACATGCCCTTTTTGGCCTCGATGGGCAGAAATGGCAGAGGTTCAAGGGGGGAGATGCTAAGATTCATGTTTTGGGGCAAATTAAATTCTCCAAAAGGGACATATGTGCAGCTTGGAATTCAGGACTCCTTAACTTTGCATGAAAGCTTCTGTCTAGATATCCAAAGGGAGGGGCCGTCTAACTGATAACGCCTGTTGCGTATCAGTCCTGCGACCCCTGGTAGGTTTGGTCAGCAGCCTTCTGTGAGGCAGGAAGGAGTCTGACCAGGGACACTCTGCAAGCTGGGACATAGACTCTGAAATATTGGTATCTCCAGAGCCAAGGTGTGAAGATAATTTTGACTTTGCTTGGTGCTGAGAAGTGTCTTAACTGGCAGGAAGGCCACCTGGCTCTTATGACCATAGTTTATTCTATTTTCTTTTTCCTGTTCCCTCTTTCTAGGCCTGGTACAATAAACTAAAAAATGGTGGGAGCCCTGGTGCTGAGAAGGAAGGAGGAAAGATATATCTACCTCTCAATAAATGTCCTCCAAGGGCCACTCTCCCGGGTCACTCGGGTGGGGGGGGTTCACAGTGGCGAAGGAGGCAGATGCGGCCTTGCTCCCTCATATGCACTCACTTGCCTGCTCTTCCAAGAGGAGAGAAAAGAAGGAAAGTTGGGGAGGAGCGGAGGAAGGAGTAAAAGCAAGTGAAAGGAAATCACTGCAGGATACAGTGGGTGATGAGGGAGGTGAGGATGATTATTTGGGTGCAACTGAGAGGGGCTTGGTTTCTCCTCGCTGGTGCCTGGGGAAGAGAGCAGTGTGGCCCACCAGGTTTCTGTGGGATGTTCCTGAGCATTTATGATCAGGTAAATTTGGGCAACAGTGGGATAAACAAAGTGAAAGAGGCTTTCTTTCTTCCTAACTAAGGCGCTTTGTGTGTCTCCAACACAAGAAAGGAAATGCAACATTTCCAAAATGTATCTGCCTGCAGGAGGCCTCTGTGATGCTGTGTCTTGGCCCCAGATTGCCGAGGATGGACTTTGGGAATATTGTCACAGTGCGGGTGCAGCTTCTGTTGTCAGGAACGTACATTTCCACAACGCTGTGGCTCTTTGCCCACTCACTCTCCTGCGCTCCAGAACAGCCTCCCTCTTTCCCCCTTCTCCCCATTCGGAGGCTTCTCTCACACCTCTCCTGACCCACCTGACTCTCAGCTGGTAATCTTGAGTCCTATTTCTCCAAGAAAATGCAAGTAAACCCAAAGAGAGCTGTCCCCGGCCACGTCATCCCGTGGTTCCTTGGGTGGCCTGTCTCCGCTTCCTCAGCTCCCTTTCCTCTCACCTGCTCAGTGGCACCATCTGCAGTTCCCTTTCTTGCTCTTGTGTCACCCTTTCTCCACTGTGCTGGATGGTTCCATCCATGATAAAATGCATTGCTTCTTCTCTCTTAAACACCCTCTCTGATGCGCCACTTCCCCTGCCAGCAGCACCTGTCTCCTAAAGACTTATCTATACTCTAAAGTTCCTTTCCTCCCATCCTCTCTGAGCCCACCCTACTTTGTCATTCACCCTTGCTCCTCCCCCAAGTGCTCCAGTTGAGGTCACTCCATCTGACAAGGTCCCTGTCTCTGGCGAAGCCCAGTGGCTGACCCTCGGGTCCCTGAGCAGCACCTGATGCAGTGCAGGTCACGTCCTTCCCAAGTACCATCCTCGCTGGTGCTGATGAGGCTCTTCTGATTCTGCCTCCGTCGGGTTTTTCATCCTTTGCTCCCCTTCTCTTTGATGTGTAAACACTGAAATGCCCAGGACTCCCACTTCTTGGACTTTTAACAGTGGTGATTGGTGTTAGGATCCCCTGCCTGTGAATCCATGACAAACTGGGCGGTGGCTCATGAACGCTAAGAATTTGGTGACGATGAAGGTGAAGCCATGCTCACATTTGTTTCGCAG
Seq C2 exon
GTGTTGGTGGCAAGAGGGACGTGGTCTTTCTCATCGATGGGTCCCAAAGTGCCGGGCCTGAGTTCCAGTACGTTCGCACCCTCATAGAGAGGCTGGTTGACTACCTGGACGTGGGCTTTGACACCACCCGGGTGGCTGTCATCCAGTTCAGCGATGACCCCAAGGTGGAGTTCCTGCTGAACGCCCATTCCAGCAAGGATGAAGTGCAGAACGCGGTGCAGCGGCTGAGGCCCAAGGGAGGGCGGCAGATCAACGTGGGCAATGCCCTGGAGTACGTGTCCAGGAACATCTTCAAGAGGCCCCTGGGGAGCCGCATTGAAGAGGGCGTCCCGCAGTTCCTGGTCCTCATCTCGTCTGGAAAGTCTGACGATGAGGTGGACGACCCGGCGGTGGAGCTCAAGCAGTTTGGCGTGGCCCCTTTCACGATCGCCAGGAACGCAGACCAGGAGGAGCTGGTGAAGATCTCGCTGAGCCCCGAATATGTGTTCTCGGTGAGCACCTTCCGGGAGCTGCCCAGCCTGGAGCAGAAACTGCTGACGCCCATCACGACCCTGACCTCAGAGCAGATCCAGAAGCTCTTAGCCAGCACTCGCTATCCACCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163359:ENST00000295550:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.010 A=NA C2=0.032
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=85.8)
A:
NA
C2:
PF0009223=VWA=WD(100=84.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Mouse
(mm9)
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
- Pre-implantation embryo development