HsaINT0039214 @ hg38
Intron Retention
Gene
ENSG00000197565 | COL4A6
Description
collagen type IV alpha 6 chain [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chrX:108162892-108164698:-
Coord C1 exon
chrX:108164600-108164698
Coord A exon
chrX:108163039-108164599
Coord C2 exon
chrX:108162892-108163038
Length
1561 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
TTTCCCCCACCTGCCCACAGGCT
3' ss Score
11.01
Exon sequences
Seq C1 exon
GCATGAGAGGTGAGCCTGGCTTCATGGGGACTCCAGGCAAGGTTGGGCCACCTGGAGACCCAGGATTTCCCGGAATGAAGGGGAAGGCAGGGCCAAGAG
Seq A exon
GTAAGTTGAGAGCATGTGCTGGGCTGATCCAGAGCTCGAGGGAGGGGCCTGGTGGTAAGGTTCCTTCAGGCATCATTGCTCACCACGCCAAGAAAGTCTGGATGTCTAAAACAGCTGGATCAAGGTACCCCAGAGAGGCAGTTTCTCTACCTTGGGGATCCTTCAGCCTCTATCACCTCCCAGGACTGAAGACCACTGCTGCCTTGCCACCATGGATCCTGCTACTGACTGCCTCTCTGTGTTAATCTCTGCATTAGTGGGCATTGGGTTTGCACTCAGATCACCACCCACCCGTTTGCTCAATTCAGAAATAAAGAACCGTCTTTTGCATCCTTTCCCACCCTCACTCACACACATGCAATCTAGTAGCAAGCCCTGAGGCTTGTACCTCCTAAATGTGCCTTGCATCTGTTCACCTCGCAGTACCTTGGTTGCTACCCCCAGATCCAAGCCACCAATAGTTCTCATGCAGCACCCTTCCTCCCCCGACCCTAGTGGTCACTTTTCCACATAGTGGCCAAAAAGAGCTTATAAAAACATAAATCATCCAGTGGCTTCCCATGGCGTAGGAATGAACTCACCGTGGCACGCAAAGCCCTGTGTGATGCCTCCCTCTTCATCCTCATGGCCAGCCCTTCCCCTTTGCTGCTCACTGTGCTCCTGCCATACTGGCCTCTTTCAGTTATCCAAAAACACCAAGTCCTGGCCTACCACAGGGCCTTTGCACATGCTACTTCTACTTCCCAGAGTGCACTTGCCCCTCTACTCTTTAAATAGCAAAGTCCTTCTAATGTTTTAGTGGTCTCAGTTTAAATGTCATTGCTTGCAAAAGGCCACTGATCATTCTCTAAAACAGATGCCTCCACCCCATACCACCCTCTGCTCCCTCCCAGTGTCCCTGTGTTAGTCCTTTCCTCCACAACACTTCTCCCAACTTACACTCAGATTAACAGTATTTGTCGAGTTAGGCATTATTCATCTTCATCACCAGACCATAATCTCCATAAATGTCTGTCATATTCATTGCTCTATCCCCAGAGCTACCAGGACCCTGGCATATAATAAGCACTGGGGAAATATTTGTTCAATGACTTACTAAGCAAATTATGCTATTAGAAAGGCAGCTGGCTGGCGCCGGGTTCCTAGGCTGGGATGCCAACTGAACCTCTGGGGTTAGAAGCGTCCCCTCAGCCTCCTTGGCACTGTGCTCTAACCAGTGAGTAAACCAGCCACCCCAGCCCTGAGAGAAGGCTCAGCTCACCATATTAGCAGCAAATGCTTCTGGACTGCCTGTCACCCACTGGGCACAATGCTGGGCCCTGAGGAGACAGGATGAATATGACCCAGTTCCTGCCCTCTTGGAGCTACCCAACCACTGGGGAGAGAGATGGATAAAGATTGTATAATATCACACAGTGCCATCCTGGAGATACCCGGGTATCCTGTGGGGACAAACAGGATAGAAAGCTGTTGATTGCAAGTTAGTAAAGAAGGCTTCTGGGGCCCCCGTCACCTCCCTCTGCCTCAGCCTGATGTTCTTATTTCCCCCACCTGCCCACAG
Seq C2 exon
GCTCTTCTGGCCTCCAAGGTGATCCTGGACAAACACCAACTGCAGAAGCTGTCCAGGTTCCTCCTGGACCCTTGGGTCTACCAGGGATCGATGGCATCCCTGGCCTCACTGGGGACCCTGGGGCTCAAGGCCCTGTAGGCCTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197565:ENST00000372216:40
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=PD(0.1=0.0),PF0139113=Collagen=FE(52.4=100)
A:
NA
C2:
PF0139113=Collagen=PD(22.2=28.0),PF0139113=Collagen=PU(53.3=64.0),PF0139113=Collagen=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTGAGCCTGGCTTCATGG
R:
CCCAGGGTCCCCAGTGAG
Band lengths:
214-1775
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