HsaINT0038191 @ hg38
Intron Retention
Gene
ENSG00000084636 | COL16A1
Description
collagen type XVI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr1:31670602-31671659:-
Coord C1 exon
chr1:31671615-31671659
Coord A exon
chr1:31670647-31671614
Coord C2 exon
chr1:31670602-31670646
Length
968 bp
Sequences
Splice sites
5' ss Seq
ATCGTAAGT
5' ss Score
10.44
3' ss Seq
CTGCCTGTTTCTCCCACCAGGGC
3' ss Score
11.94
Exon sequences
Seq C1 exon
GGTCCGCCTGGCATGAGGGGCTCCCCGGGTCCTCCAGGCCCTATC
Seq A exon
GTAAGTATCAGTGGTGCCCTGGTCTGCTTGAGAAGCTCTCAAAGGGGTCATTACACTCAGACACCATCCCGCGGCCTTGTCCCCAAAAGGCTGGGCAAGGCAGGAGGAGGGAACTTCCACTGCCCTCCCCATCCCTCCGCAGAGCATCTGCAGGGACTGTGCTCTCCCACCACCGGATGCCCTGGAACCGCCCTGCTCTGCCTACTGCCTGCGGTCCTGCTTAGGGGAGGTCCTCAGAGGCACCTCTTTGCTTCCCTGTCCCCACCCTCTGCTGCGCTTTCCACAGTGGCCCCAGGCCGCCCTCGGCAGGGGGCCTAGGCTTCAGGCTCACAGCCTCCCAACCAGGGAAGCATGCGGCATGCTGGCCAGACCTCTCCATGCCCCTGTGACTCCAGTCCCCACAAGGGCTCGGGGCTAAGATGGAGCTGTCCTCCATTGCTCTGTAGGGCCATCTCTAGGGTAAATCTACAAAAACCAGACCAGGGTATCTACTCTGGAGTCCTCTGTGATGTTGACATGGCAGGAAAATAGAAGTGACTAGGAAAGATTGAAAGAACTGAAAATGCTTTCTCTGGAGAAGAAAATGGCTGGTGGGAGCTGTCTTAGAGCCAGGGAGCCCCCCACTCGGGGGACAGGTGGAGGTCGGGTGGCAGGCATGGTGGGCAAGGCTGAAAGAAATGGGCTTCTGCTGCAACCGGATCTTCAGTTAGACTCCGGAAGACTCAGGAAGCCCTCTGACTCTGGAGCCATTCCGCATCTCCGTCAACGGAGGAGCCATTCTTCCTGGAGCCAAGGGGAGGAACAGTTGTCTTTTGAGCCAAGACTTTCAAGGAGTCTCTTTTCCAGCTGCCTTGAAAATACTCCCATGACCTCCTCTCCCCATGACCCCCAAGCCCCAGACTGTGCCCTCCAGGCTGTCCCAGGGTTACTGTGCCTGTGAGATGTGACCTGCCTGTTTCTCCCACCAG
Seq C2 exon
GGCCCCCCAGGTTTTCCTGGTGCTGTTGGCTCCCCCGGATTGCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636:ENST00000373672:48
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=FE(20.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.3=100),PF0139113=Collagen=PU(15.7=73.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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