HsaINT0038769 @ hg38
Intron Retention
Gene
ENSG00000196739 | COL27A1
Description
collagen type XXVII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:22986]
Coordinates
chr9:114304608-114306688:+
Coord C1 exon
chr9:114304608-114304673
Coord A exon
chr9:114304674-114306519
Coord C2 exon
chr9:114306520-114306688
Length
1846 bp
Sequences
Splice sites
5' ss Seq
GAGGTATCT
5' ss Score
7.27
3' ss Seq
CCACCCTCTCCTCGTGACAGAGT
3' ss Score
7.66
Exon sequences
Seq C1 exon
CAACAAGATGATCTTGGGGCAGCTTTCCAGACGTGGATGGACACCAGTGGAGCACTCAGGCCAGAG
Seq A exon
GTATCTCCAGGGGCTCTCCCCATGTGGGATCCCTTCCTGGGAGAAACGCAAATAGATAATGGCCCACATGTGGTCAGTGCCTTCCATGTGGCCTGCATGGAGCATTTCAGAGTCCTGGTCTTGGTGGCATCTCGCATCCACAAATGGGGGTTTGTACTGAAACTCAGAATGGGCAGTGAGTCCAAGGTCCCATGGCCAGTGCAGGCAGAGCAAGGCCAGAAACAGGCCCTGAACCCTTGAGCTTTCTCCGGAGGCCTCTCAGAGTCTCCAAGCTCTTGCTGGCTGGAGTCAGGGGGAGAAGCTTGCCTGGGCCCAGAGCCCGCAGCAGCTTCCCAGTGCTCATCCCCACGTTTCTTCAGGAGTAAGAAGCTCATGGTTAGCTCGTGGGGCTCTGCTAAGAACCTGCCCTGTGGTTAACTCAGCTGTAAGACTCCAGGCTGAGAAGGGAGTCCCATGTCCTCTAGTCCAGCCTCGGTCAGGAGCCCCCTTTGCAGCCTTGCCTCCTTCACATGACAGGGAACTTACTGCCCCCAGCTCAAACCTCCTATGAACATTTCGGTTTGTTCCCTGTGCTGGATGCTGAGACAGATGGATGGCCAGTCACAGCCTTGACTTTCAGAGGGCTCACAGTCTAGGGTGGAGGACAGCATGGATGAGCCCCTTACCATCTGTCCGGGGAGGTCAGTGGAAAGAGAGGGGAACACTCAGGATCCAGTGCGGCTGGAGAAGGGAAGCGTTTCCTTCCATCCCTAGAAGCCAGTGATGCCGCACAGGAGAGCGCTGACCTGCAACATCCTTAACATGATGAAGGAAAGTGGCTCCGTTTATCAAGCACCTCCTACCCACTCTGCATTGGCGGTAGAATAGAGGCTTATTTCTCGTGCACGTAAAAGTTAATTGGCTTGTTGATGAGAGACCTTGGCTACCTGCCAGGGGCTCTGCCCTCTTCCTCTCCCACACGTGGCTCCCAAGGTCACTCCACACCAGGGGGAGGCACCACCGGGGAAAGAGAGTGTAGAGAATTGTGCAGGAGGGTCTCTGGGCCAGGCCTCTATGGGGCTAGCATCGCTCCACTTCCATCCCGTTGGCTAGAGCACAAATAAGGCTGAAGATGTAGTCTGTCCAGGCAGAAGAAATGGATTGGGTGAGCGGCTGCTGGTCTCTGACACACGTTCACACATGCGTGCACACACACACGTGACCTCCGCCACCCCCAGTGGAAGGAGGGTTTATTTAGCTCTGATTTGTAGCTCTGGAAGCTGAGGCTTAAGGGAGAATTCTGGCCAGGGTAACCCTGAATGGCCGGCTGTTTAGCATCTGTGGTCCCCTCCTGCCCCCTAGTGGAGATCTGCTCCTTCTCTGAGCTGAAGTCCTCCTCCCAGCACTTGTGCCTGCTGGCCCCAGTCCCGTCTCCTGGTGCCTCACAGAGACCCTGGCTCCCACCCTAGGGGAGCCCAGTGGGGGCTGTGTGACCCCCAAGTCAGCTCCCCCCAGCACCTCCCCTTCCTCCACAGGCTCTTTGCAGATAGAGATTGGGCCGCTGCCGAGTGTCCCACGCACCCTCGCCTACCTCATTCACGGGGCTCTGCCTGTCCCATATCAGAGAACATGGTCTGACCCTGAGCTCTTTTCAAGCCTCTGAGCCATTGTGATAGCCTCTCCTCCTGCACTTTGTCCCTGGCCCGTTTTCTTGTCTGCAAAATAAAGAGAAACCCAACCCGTGCTCTAGCCATGACCGTGGAACCGAGATACCTCCCAGGTTGTGAGAACTGGGGGCTGTGGAGGCTTGAACCCCAGGCTGGACCAGGACCCTAAGGTCCCAATGACCACCCTCTCCTCGTGACAG
Seq C2 exon
AGTTACAGCTATCCAGACCGGCTGGTGCTGGACCAGGGAGGAGAGATCTTTAAAACCTTACACTACCTCAGCAACCTCATCCAGAGCATTAAGACGCCCCTGGGCACCAAAGAGAACCCCGCCCGGGTCTGCAGGGACCTCATGGACTGTGAGCAGAAGATGGTGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196739:ENST00000356083:57
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.782 A=NA C2=0.225
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0141013=COLFI=PU(39.1=47.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGATGATCTTGGGGCAGCTTT
R:
CATCCACCATCTTCTGCTCACA
Band lengths:
230-2076
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