HsaINT0039549 @ hg38
Intron Retention
Gene
ENSG00000172752 | COL6A5
Description
collagen type VI alpha 5 chain [Source:HGNC Symbol;Acc:HGNC:26674]
Coordinates
chr3:130406268-130409388:+
Coord C1 exon
chr3:130406268-130406321
Coord A exon
chr3:130406322-130409325
Coord C2 exon
chr3:130409326-130409388
Length
3004 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
ATTCATTTCATTTTTTTCAGGGC
3' ss Score
9.4
Exon sequences
Seq C1 exon
GGCTGTCATGGATTTCCTGGAATAAAAGGAGAAAAAGGTGATCCAGGATCTCAG
Seq A exon
GTAACACTTTTCTTTTCAATACTTCAAAGAAGGAGAATTTGGTGACAGAGACAGTCTTAACTGCTGTGTGTCAGTGGTTATAGGGGATAAAATTTACAACTGACTTAACCACATAATGAAGGCCTATTGCTACTGAATGTATGCTGCATATCTGATTGAAGCAAGGGGGTAATTATGTAATTTTAAAGAATTTCCACCTAGAAAAATTTAGCACACACAAGCTTGTTCTATGGGCATGTTTCTCATGTCTGAAAATGAATGCTTTCACCTGTCAGTGGTTTCTTTTGTTCATTTGTTTTTTACCACAACGTTTCCATCAATGTCAGTAATTTCTGTGTTGTCTTTATTATGTCAGAAAAAAAAAAGCAAGAGAAAGAGACAAAATTATTTTGGTGGCTTTGGTAGCAAATCACTGTGAAACATTTTTTAACTTTACATTTATTTCAACACTCATTAGTGTGTGCCTACTTGATTTCAAGCAGCTCTACTTTTATGTTCTGATCCATTGATTTATGAAATATTTTTGAGCACCTGTCATTTGACAGGTTTGTCATGTGCCAGGCACCTGTCATTGGCCAGGCATATATTCTTATATAATAAGAATCAGAGGTGAACCACACAGCCCTTGTCATCAAAGATCCCACAGTATAGTTGGGGAGACAGACATATCAATAGAATTACATAAAATGTGAGTGAGGCCATGTTGTAGATATCTACATGGGAGTCCAGAGAAGGGCATGTAACTCAGCCTGGGGGCAGGGGTTGTCCAGAAAGTCTTCCTGGAGGAAATGACTTCTGAGCTGAAGAGGAACAGGAATTCAGCAAGGCAAAGATGTGGAGGAAGGGCATTCCAGACAGAGGGAGTAGCATAAGCAAAAACATGAGGGTTCAGGGCACTGCCAAATTTTACTTCCTGGAGGGAGCATTAGAATACAGGTACTGGGAGGTGAGGTTCAAGAGGTGGTGGTGGGAAGAGATCAAGAGATTGGGAGGGCACTAGTGAGCCATGTGGAAGAGCTTGGTTTTTAACCGTAAGGCAATGGGGAGCCTTTGAAAGATTTTAAGCAGAAGAATCACAATCAGATTTACATTTTAGAAATATTACTTGCAGTAATGTGGACGATACTTTGCAGATGACATAGATGCAAGACAAAGATGAGAGGCAGATCTGTAGAAATCAGGTGAGAAGTGATGAAGCCTTCAAGTAAAGCAATGATAGTGAGAACAGACACAAAATATGCTAAGGGTGTAGCGGGGTTTGGACTGAAGTGAGGCTAGCAGGGCACCTAAGGTGCAAAAGGGGCAGAGTTATGTGGAGTAAATACCTACCTCCATTCTGCACCTTAGGTGCCTCTCTCATCTCACACTAGTCCTGGTTCTAGGACCTGAAATCTCCAGATATAGGTGACTAGAGGAACAGAAAATAGAGAGTCAGTCAATATGCCTGCAAGGATCCTGGCTTGGGCAAGTTTAATCGGAAATAATTAGGTTTGAGGTGACAATGGAACATGTTGCAGGAAGTCAGGGAACCCGAACAGAGGCTGAAGCCACAGCAGAAGAACATAAACTGTGAAGATTTCATGGACATTTATCACTTCCCCAATGAATACTCTTATAATTTCCTATGCCTGTCTTTAATCTCTTAATCCCATCATCTTTGTAAGCTGAGGATATATGTCGCCTCAGGACCCTGTGATGATTGTGTTATCTGCACAAATTGTTTGTAAACCATGTGTGTTTGAACAATATGAAATCTGAGCACCTTGAAAAAGACAGGATAACAGCGATTTTCAGGGAACAAGGGAGATAACCACAAAGTCTGACTGCCTGCGGGGCCGGACAGAACAGAGTCATATTTCTCTTCTTTCAGAAAGTGAATAGGAGAAATATCGCTGAATTATTTTCTCAGCAAGGAATCACCCTGGGAAAACGAATGCATTCCCGGTGTGGGGGTGGTGGCAGGGGGTGGGGGCGGGTCTCTAAAATGGCTGCTCTGGGAGTGTCTGTCTTATGTAGTTGTAGATAAGGGATGAAATACGCCCTGGTCTCCTGCAACGCCCCCAGGCTTGCTAGGATTAGGAAATTCCAGCCTGGCGAATTCTAGTCAGACTGGTTGTCTGCTCGCGAACACTGTTTCCTGTTAAGATGTTTATCAATGACAATGTGTGCCCAGCAGGACGTGGACCTTCATCAGTAATTCTAGTTTCGCCCTGGCCTTGTGATCTCACTCTGTCTCTCTGCCCTTGTGATATTTTATTGCCTTTGAAGCATATGATCTCTGTGACCCACTCCCTATTCGTACACCACTCCCCTTTTGAAACCCCTAATAAAAACTTGCTGGTTTTGTGGCTCAAGGGGCATCACAGAACCTGCCGACATGTGATGTCACCCCCAGAGACCCAGCTGTAAAATTTCTCTCTTTTGTACTCTTTCCCTTTATTTCTTAGACTAGTGACACTTAGGGAAAATAGAAAAGAAACTACGTTGAAATATTGGGGGCTGGTTCCCCCGATAGAACATCCCTGTGGAAGTTTTCAGTGGGCAATTTAATTATAGATGTTGGAAGTTGCTAGACTGGCTAGGATGTCCAATACCATAGCCACTAACCACATGTGATTATTTAAAGTTTAATTTTAATTAATTAAGAAATTCTGCTCTTTAGTGGCATTGATTACATTTTATGTGCTTAATAGCCACATATGGCTAATGGCTACCGTATTGATGAATGCAGATATAGAACATTTCCATCACTGCAGAAACTCCTATTGGACAGTGCTATGTTAGACCACGAGAAGTTTTCCAGTTTCTGAGCCTCGCTACAAATAATCCTGACCATAGGCTTAAAACTGGACTTAGTACTGCTTGAGAAGTCTGAGGGAATCTGACTGTGATAGGACAAAGAGCATTTTATCTGATTAACCCCCCTACATACAAAACTTCACACTTAACACCATTATACAAGCCTCCTACAAGCTAACTCAGAAATTCATTTCATTTTTTTCAG
Seq C2 exon
GGCAGCCCAGGTTCCAGAGGTGCCCCTGGGCAGTATGGAGAGAAGGGCTTCCCAGGGGATCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000172752:ENST00000312481:17
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(23.9=100),PF0139113=Collagen=FE(28.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(33.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
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