HsaINT0038769 @ hg19
Intron Retention
Gene
ENSG00000196739 | COL27A1
Description
collagen, type XXVII, alpha 1 [Source:HGNC Symbol;Acc:22986]
Coordinates
chr9:117066888-117068968:+
Coord C1 exon
chr9:117066888-117066953
Coord A exon
chr9:117066954-117068799
Coord C2 exon
chr9:117068800-117068968
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-COL27A1:NM_032888:57
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.626 A=NA C2=0.123
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0141013=COLFI=PU(39.1=47.4)
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:
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
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)