HsaINT0038730 @ hg19
Intron Retention
Gene
ENSG00000196739 | COL27A1
Description
collagen, type XXVII, alpha 1 [Source:HGNC Symbol;Acc:22986]
Coordinates
chr9:117002714-117004511:+
Coord C1 exon
chr9:117002714-117002767
Coord A exon
chr9:117002768-117004466
Coord C2 exon
chr9:117004467-117004511
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-COL27A1:NM_032888:21
Average complexity
IR-S
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(15.2=55.6),PF0139113=Collagen=FE(27.0=100),PF0139113=Collagen=FE(19.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.7=53.3),PF0139113=Collagen=FE(16.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)