HsaINT0038187 @ hg19
Intron Retention
Gene
ENSG00000084636 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:2193]
Coordinates
chr1:32138325-32140640:-
Coord C1 exon
chr1:32140608-32140640
Coord A exon
chr1:32138442-32140607
Coord C2 exon
chr1:32138325-32138441
Length
2166 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TCTCCCCACTCCCTGATCAGAGT
3' ss Score
8.29
Exon sequences
Seq C1 exon
GGATCCTTACCAATTGAACAGCACCTCCTTAAG
Seq A exon
GTAAGAGGGTACCCAGGAGGGAAGTGTGAGCTGGCGGGGGTGTCTCCTAAGGGGATTCTCTTAGTAAGTGCTCAGCTGTGTGGCACCTCGCAGAGAGAGCAGCAGTTTGCAGGGAATACGCATTCCAAGCATCTGTCTAAGAGGGCCTAGCTGATGCCTGGCTTGTAACAGGCCCCCAGGCAACATTTGCTGAATGAGTGCTTAAAGGAATCCTGTGAAGGTGCCCACATGGCAGATGCTGTCGGCAGAACCCAGCCCTGAAGCCTGCCCGCAGCAGCTGGCAATGAGACCCCGTAGCACCCGGGTCACCCTGCGGCAGAGCCCAGCAGCTTCCAAAGCAAAGCAGAGGGGGTGAAAGTGCAGTGGTGGGGGGCTGTGAGATTGGGTGTGGCCTGGAAGAAAGCTTCAGCTGTTCTCTAGTCAATCCAGAAAGAATCCAGGGAGGAGATGGATTTGAGAAGCACTTCTGGTAGTCTAAGAAAGGGGACTTCGGACCTGGTCAGAGGGTCGGCCTGTGCCAGGGCCTGTACACAGCCTTAATGCTCTACCAGAGGGCTGTGGCCTGGGCCGGCTTCCCAAACTGAGCAGAAGTTCCTATTGGAATCAAGAGTCACATAGCCCATCTTTGCTTAGTCACCTCTAGAAACGAGAGCACAGTAATTCCCCAGGTTGCCTTCAGGTTTTTGAAGGAGGCCCTTATGTTCCTGGACTTTCTCTCCTCTAGCCCAGCATCCTCAGGGGTCTTTCCCATGTGTTGGCCTCCAGAGCCCCCCCTCATCCTGGCCACCCTCTTCTGACACTGGCTAATTAGTGCCCTGGACATCCCATGACCCCGATGGGCCTTGGTCAGGGCAGAGCATGGGGGCTGTCTACCCCTTCCCTGCTCTGAACGGCAGATTTCTCCAGAAGCAGCCAGAGGAGGTCGGGGTAACCTCTTGGCATCAGTTACATGTTGGATCACAGTGAGGTTGTGGCAACGAAACCCCCAGCTCTTCTCCCCTCTGCTTCTGTCAATGACTGGGCAGTGATCGTGTGACTCCAAATCCAGGATTTGACATTTCTCCTGTAACATTTCATCTGTTGGCTTCTTCATCAAGTGCTCTTCAGAGGATTCCAAATAGAAAGTGCGCATAGTGTGGAGAAGGGGTCAGATGGCACCCCGGGGCATGCTGACCCAGAGCCCCAGCCACCACCTGCACCCATAGTCCAGGAAGCCTGGGGAGAGAGCACTGGCTGTGGCCTAGGACAGGCCCACGCCAATCCAGGCTCCCACTTTCCTTAGACAAGTCACGCCGCCTCTCTTGAGTGGGCTTTCCCATCTCCACAATGCTTATAAGATTCCCTGTCTCACTGCGCCGTCAAGATGGCATGTGATAATGTGCAGGGCTTATTATGTACAATGCCCAGCGTCATGGGTGCTGAGTAAATGCCAGTCGTTATTACTGGGCTTGGTGGTGAGCAGTGAAAGTGAGCAGGGGCTCCTGCCTGGGCATCTGTGGACACGACACTGGCCACAAACAGGCTCCGGGCTCCTGAGTCCTCAGAAATTGCAGGCTGGTTTTCACTAGTGGGTTTGATTTTTCTGAGAAAAGGACCCATAGCTTCCATCAAACTCTCAGAGGGGTCTGTGACCCAAAGAAGGTTAAAGCCCTTCCTGTGGGGAAGACAATTCTGGTGGCGCGATCCGAGCCAGGAGCCTGTGAGCAATCTGAGATCTGTCCCAGGGGCTCCTGGGAAGGGCCTGGCTCCTCCCGCAGCTGTTCCTTTGCTCCCTTGGGCAGAGAAGCTGGCGTTCGGAGCCAGCCTTTCCAGCCTCACTCCTCGTGGCTTGTCCTCGCAGTGGGTGCAGGTTGCAGGAACAGCCGGGACAGATGGTCCCTCTGCGGGCCCCTCGCCTCCACCCACATGCCTGTCTGGAAAGTGGCTTTGGCTTAGCTGTACCAGAGCTTCTTCCTGGAGGAAACTCAAAGCCAATTGTTGGGAGTGGGTCCCCCGAGGATGGAGCAAAGCTGCCGCAGGGATGCGGCTGGGGAGGGAGGGAGTGTGGGAGGAGGGAAGACGGCAGGGCAGGGAGCCCTGGCTCTGGGTTCTCACTGGGGCTCCCCAGTTGGCCCATCCTGCCCATCTCTAACCCAGGCCCCACTCCTCTCCCCACTCCCTGATCAG
Seq C2 exon
AGTATCTGCGGGGACTGTGTCCAGGGGCAGAGGGCCCACCCAGGGTACCTCGTGGAGAAGGGAGAGAAGGGAGACCAGGGCATCCCTGGTGTGCCAGGCCTCGACAACTGCGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636-COL16A1:NM_001856:44
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.364 A=NA C2=0.628
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(4.0=18.2)
A:
NA
C2:
PF0139113=Collagen=WD(100=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
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)