HsaINT0038744 @ hg19
Intron Retention
Gene
ENSG00000196739 | COL27A1
Description
collagen, type XXVII, alpha 1 [Source:HGNC Symbol;Acc:22986]
Coordinates
chr9:117029784-117031574:+
Coord C1 exon
chr9:117029784-117029837
Coord A exon
chr9:117029838-117031520
Coord C2 exon
chr9:117031521-117031574
Length
1683 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TTTTGTTCGGCTTCTCCTAGGGT
3' ss Score
7.64
Exon sequences
Seq C1 exon
GGGCCGCCTGGTGCAGTGGGAGAACCGGGCCTTCCTGGGGAAGCCGGGATGAAG
Seq A exon
GTGAGGTGGGATGAAAGAAGAGAAAAATGACTTGTTGAAACCAGCTCCCAGATGGTGGCCACATCCTCTCCATGGAAGAGAAATGGGCCTTTCTTGTGGCTGGGATAATGGGTTCTCTGTGCTCCTGGCTGGGGAGTGGGGCCTGGTTAGGGCCAGAGTGGAATGTGGAGCCCCCACCAGTGCCCTCTGCGAGGTAATGTTTTTTCGGGCACCTGCCCCTGCCTCTATGCTGGGGTGGCTGTACCTCCTGGCCTCATGCGATACCATCTGCAGCTCGGTGCCAGTGCCCTTCATTACCTGCTGAGAAACAGGTGCCCATTGATACATGGACTCTGGGGAGAGCCCCCTCCCCATTCTGCTGTTGGAAGAGGACGCTGTTCCCCCTTGGAGGCCCCAGAGCTGATGAGTGATGCTGGCTAGCCCGTGGACATTGTTGAGGCAGGGCCCAGGGGAGCCCGCAGAGGGGCTGTGAGACTTGAGTCCAGTCACCCCCTTCCATGCCTAAGTCTCCCTGTCATTCAAAGAGGGAGTTGGACCAGGCCGGGGGCTGCCAGACTTGGCCTAGTCCCAAAATCCCTTGCTCAAACACCAATGAAGAAAACCACCCCACGTAGAAAACTGATAGAAGTGGGATTGTTTCCACTGGAGCAGGGCTGGGGGCTCAGAGCTCTGCCCTCCTCCTGTGCCCCTAGACACCAGCAGGGAGCATAGCTTGAAAATTCACCAATGAAGAAACCACCCCACGTAGAAAACTGATAGAAGTGGGATTGTTTCCACTGGAGCAGGGCTGGGGGCTCAGAGCTCTGCCCTCCTCCTGTGCCCCTAGACACCAGCAGGGAGCATAGCTTGAAAATTCTCCAATGAGAAAGACCCTTTTAGGGCCTTTATGCAGGGGGCAGGTGACATTTATTCCGGCTCATTTAGGGCTTCCTCCTCGTTTGGGTTTCTCTTCAAGTCTCTCAAGGAAGAATAAAGTCACATAATTGCCATTGCTGCATCCAAGGCTCCTGGAACCAGACTGCCCAGGTTCGGATCATGAATCTGTCACTGAATAGTCTCACGAGAGCTTGGGCTCCTTACCGAACTCCCCCAATGCCTCTGATGCTTCACCTCTAAAATAATGCCTTTCCTTGCAGGGCTGTCTTGAAAGTCAGATATGTTAATATAAAAACTGATGTCCTCAGCCTGGGCAACGTAGTGAGACCCCATCTCTACAAAAAATTTAAAAATCTGCCGGGCATGGTGGCGCATGCCTGTGGTCCCAGCTACTTGAGAGGCTAAGGTGGGAGGATCACTTGAGCCTGGGAGATCAAGGCTGCAGTGAGCTGTGATTACCCCACTGCACTCCAGTCTGGGCGACAGAATGAGACCCTGTTTCAAAAAACAAACAAAAAAAGTCCTTAGAACAGTACAGAACAGTACAGTTAGTTATTAATAGGATGATGGTGTTGGTGCTAATTGTCCTCCTGTCCTGGCGTGGGAGAAGAAGTCCGTGGACAAGGCTTACTTGGAACAGGAGCTCTGGTTGGTGTTTTACGATTTCTCTGTGGTCCCTGGGAAGAAGGACCTTCCCCAGCTCCTCCTCCCACACCCCAAAGTCAGAGCTGGTGGAAACAGGAAGGGGTGTCGAGAGCTGGGGCTGGCCCTACCCACCCGCAAGGACTTTTGTTCGGCTTCTCCTAG
Seq C2 exon
GGTGACCTTGGACCCCTGGGCACTCCTGGGGAGCAGGGCCTCATTGGGCAACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196739-COL27A1:NM_032888:34
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.991 A=NA C2=0.912
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(20.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.5=100),PF0139113=Collagen=PU(19.2=83.3)
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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
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)