HsaINT0038161 @ hg38
Intron Retention
Gene
ENSG00000084636 | COL16A1
Description
collagen type XVI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr1:31690529-31691226:-
Coord C1 exon
chr1:31691188-31691226
Coord A exon
chr1:31690574-31691187
Coord C2 exon
chr1:31690529-31690573
Length
614 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATCCTTTCTTCTGACCACAGGGC
3' ss Score
8.26
Exon sequences
Seq C1 exon
GGGGATCCAGGTGGCCCACCAGGCCCCAAGGGAGACAAG
Seq A exon
GTGAGCATAGGTGGGAGTGTGGTCACGTGGGGAGCTCCATGCTTGACAGGAGGAGAGAGAAGGGGCCGGGGCAGCTTCCCACAGGGGAAGCAAGTCCCAGGGAGGAGGCCGGGCCTTTGGAGGAGGAGGCTGGGCTCGGCTTGGCCAGGCCCCTTGGCGGGGAGCGTCCTGTCCCCATCCCAGTGCTCACTGAGCTGCTCACTGCAACCTCCGCCTGTGTTCCAGGTATAGGGATGGGCAGACCTAAGTGTTGTAAAGATCAAAGTGGACTTTGCTGGAGGGCCCAAGCTCATTTTAGAGCCTTGTGCCTGGATGTGCAGAAAGCTCTGGAAATTTCTGTCTGTGACTGCTGGGGTCACGCGGATCACCTCTTAACCTGTGCACCAGTGAAGGGGCACACAGAAGCTTCATTTTCTCCCTTCCTTTGAAACCTAGAATGGCTTGGGTTAGACACGGAGGGCAGGCAACAGGAACCGACCGAATGGAACAAATGGCAACAAGAGATTTGGCAACGATTGTTCTGCCATCACAGAGGGGCACGGGTGGGGAAGGGGGAACGCACCGAGATTGCATTGGCCAGAAGGCTCCCCGCTTATCCTTTCTTCTGACCACAG
Seq C2 exon
GGCAGCTCGGGGATCCCAGGAAAGGAAGGCCCTGGTGGGAAACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636:ENST00000373672:20
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(4.5=23.1),PF0139113=Collagen=FE(21.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(24.6=100)
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
- Autistic and control brains
- Pre-implantation embryo development