HsaINT0038730 @ hg38
Intron Retention
Gene
ENSG00000196739 | COL27A1
Description
collagen type XXVII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:22986]
Coordinates
chr9:114240434-114242231:+
Coord C1 exon
chr9:114240434-114240487
Coord A exon
chr9:114240488-114242186
Coord C2 exon
chr9:114242187-114242231
Length
1699 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CTCGTGTCTCCCAATTCTAGGGA
3' ss Score
10.51
Exon sequences
Seq C1 exon
GGTAAGCCTGGAGCCCGAGGCCTGCCGGGACCCCGTGGGCAGCTGGGGCCCGAG
Seq A exon
GTGAGACTGTCTGGCCCCCTCCACTGCCCATCCTGGCCTGATTGCAGCCCCCAGCCTGCCCTGTCCTGGGTACTGAAGGCCTTAGCTTGGGCTGGAGCCCCCTCAGCCAGGACACCACCCAGGGCTTCCCCAGACTTACCCACCAGCTCATCCTATACAGCCCTGCCCCGTGCCCCTTCCAGGGACCTTCTCTGCCCTGCTGTCACCTGGCAGGGTGGCTTCCCCGCACCCTCCCTCCTCTGCACCCTCGTCACCCTGGGGTTTTCTTTCCCAGAGCTACTGACAATGCCGTGCTCGTGGTAGCAGTTTATCAGGGCATTAATGAGGGAGTAGGAAGTGTCAGCCCCATTTTACAGATGAGGCCACTGAGGCCCAGAGAGGAAAAGAGACTCAGTCAGGTCTTATGGTTAGTAGCAGGCAGGGCTGCAATGGGAACCCAGGTCTGCTTGAGCCCAAAGCCCATGACATACGTCCTATGCTGTCAACTCTGTGCTTCCTGGGAGTGGCCTTGCTGTCAACTCTGTGCTTCCTGGGAGTGGCCTAGGGGCACCTCCAGAATATTACAATGACTTGCACAATTAGTTAGTGGCAGAGCATCGATTTGCTTATTTATGTGCGCTGGATGAAGTGGGTTGGGAGGGGTCTCTATGGGGCTGTTGGAGCACCAGGTGGGCACTTAATGGGTGGGCCCCTGATTTTGCCCTGTGCACGAGGCCATTCTTAGCCTTCCCATGCCCCACCTACCTTAGCTCAGGCGCCAGGCCCCCGTGACACACAGCCCTGGGCTGAGGGTGCGGGAAGCCCAGATTCACCGCGACCGCAGGCGGGCATCCAGCTGACATGGATCCCTTCTCGGGCTGGCTCTGGGTCTGGCGGGGTCCCAGCACTGGCTCTGGGAGCCACCACGTGGAGCTGCTTTCCTGGAAGCTGGGGAAAAGGAGCTGGGGGGTGTCTCTGGAGGGAGCCCCTTGGTCAGGCCTGGCATGCCAGAAGGAGCCAATTAGGAGGCTGCCTGAGCCTGTGGGGGTGGGGAGCACCTGGAGAGTCTCATGGGCCGGAAGCGGGAAGGAAGGGGAGAGGAGGGAACGGCACCAGCCACATGCTTCTGTCTACACTCACATTACCACTCAAGAAAGCCCTATGTATGCCTGCCACTTGTTCACATCTTCATTCATTCATTCATTCACTCACCAAACACCCCTTAGACACGGCACCATCCCGAGTGATGTTTGGGGGTGGCTGCAAGAAAGAATAAGGCATCACTGCTGACCTCCAGGAACTCAGCTGAAGCCACTTATTATATTTGAGGATGATCTTCTCCAATCTGGGAAACTGAGACACAGTGAGGCTGAGGTCTGCCAGTGAGCAAATGGCAGAACTCAGAGCCTACATCTTTGAGCTGCAGTTTGAGGCTCTGTTCCTCACAGCACACAACGGGGTTTAACTCTCATGCCCAGGGCTTCCATGAAGCCTGGAGTCTCCATTCACTGGAAGTCACTGTGTAGCCTGGCCTCTAGGCCATGGCCAGTGGAGCCTCTGCCCTGGGTGGGGCCAGGCAGGTGGGCCAGGCGTGCTGTTTCCCTTTGTCCAGGAGGGCTCTCCTCTGTCCATCCCTTTCCCTCCATACAGGACAAGATCTCTGCAAGTCCAACTGGATTAACTTTCTCCTTTTTTCCTCTCTCGTGTCTCCCAATTCTAG
Seq C2 exon
GGAGATGAGGGACCCATGGGGCCGCCAGGGGCCCCTGGCTTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196739:ENST00000356083:21
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(14.8=50.0),PF0139113=Collagen=FE(25.8=100),PF0139113=Collagen=PU(26.6=94.4),PF0139113=Collagen=PU(2.7=11.1)
A:
NA
C2:
PF0139113=Collagen=PD(16.7=73.3),PF0139113=Collagen=FE(21.9=100),PF0139113=Collagen=FE(18.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
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
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development