HsaINT0038192 @ hg38
Intron Retention
Gene
ENSG00000084636 | COL16A1
Description
collagen type XVI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr1:31668802-31670646:-
Coord C1 exon
chr1:31670602-31670646
Coord A exon
chr1:31668856-31670601
Coord C2 exon
chr1:31668802-31668855
Length
1746 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGA
5' ss Score
4.07
3' ss Seq
TCATGATTTTTCTCTCCAAGGGC
3' ss Score
6.97
Exon sequences
Seq C1 exon
GGCCCCCCAGGTTTTCCTGGTGCTGTTGGCTCCCCCGGATTGCCT
Seq A exon
GTAAGAACCTAGCGCTGCTCGACCTCCCCTCCCCCCCGTCAGCCAGGTCTCTGTGGCTTTTGCTTGTCTCCCTCCTGTCGTGCCTTCACCTCCGTCCTCCGTGTTTGTTGTCCCCCTTCAGGCACGGTAGCTAACGACACGGGTTCTCTGAGGTCCCGGCAGCTTGGACATCCTCCCAGTCTCTGACTCCTTTCCGTTTTCTCCTCTCCCTCCTCTCCTGCGTTCTTTCTCTCCTCTTCTCTCTCTTACCCCGTTCTGTCTTCCTTCTCCATTTCTCGCACCATCTTGCAGCACTCCCCCAAGTCCTCCTGAGCTCGTGAACCTTCCTCTTAAGCTGGTGCCTCTAGGGGGCCCCTCCATTCCTGCCTTCTCGCTCTGCCTCCTGCTTCTCACCACCTTCGGCGTTGCCTGAAGATTTGCTGAAAGTAGTTCTTGGGGCCCTGCCAGGCACCTGGCTCAGAGCCCAGCAGAGATGCCAAAGCTTTAGGGCTTCACATTGCAGGCTGGCACAGGTTTGCTGCCCTGCTGCTTGGCAGGGCTGTCCAGAGGCACCCAGGGATTTAAAGGCAGCCCTTCCTGCGCCTTTTCCGTCGTCCTAGAGGAAACTCTCAGCTGCCTCCTCTTCGCTTCCTCTTCCTTGGCTCCAGTCCCAGTCTGCTCCAAGGCGGGGCATGTGATATCAGCCAGTTGGGTTTCTGGGTGTCGTGCGGCCCTGCCCCTCTGTGCCCGGCACCTTGGCCGGCTCCTTCTGCCAGGTGTCGTTAATTGCTCTGCCTTCGTCATCGTCACAGGTGTGTTTACATCACCCCCAGCCTCATTGTTGCTCCCTCCTGGGTCACGGAAACTAACCTCCTGTTTGTCAGGTTTTGTGTTCCTGGGGCCTGGCTCCTCTCCTCCCAGGCCTGGTGATGGAGGCTCAGGGAGCAGGGCCCCTCCTCGTCACAGTTCCATCTGTCCCCACGTCCTCATCTGTGGCCGGGCCTTGTCTGTTTCTGCTTGCTTGGGTGAAGGGGCCATCTGTCCGTCTAGCCATCTGTCTTATGTCATGGAAAGGTTTGGGCGTCATCTCTTGAGGGGATGAGGGAGAAGGGGGCAGGAAAGGTGCCCTTAATGGCATGGCACCTGCAAAGGCTGGGGTAAGGAATTAGGGGTGGGGGCTGTAGCTCTCGTGGAAAGTGACATGCCCTCTCACCCTACAAAGTGACAGGGACTGCTCTGGAGGCAGCCTTCCTGTGTCTCTCCCCTGCCTCCCTCCAAGAAAGTGATTTTTGCTTGGGGTGGGGGACTTGGACAGGTAAGTGTTGGGTATCTGATGATATGATACACTTTGGTGGCAGCATCCATCTGGGGTACCTCTCCTGACAGTTGCCCCTCAGAATAAGCACACATCTGATCCATCACCTTCCTAAAGGTGTACGCCAGTCAGTTACCATGGCAGGGCATACCAGCGACGGGCACCTGAGAGATACCCTCCCAGAGTCACCTCTGCTGGAGGGCATATCTCTATAGTTATCTATCTTGAAGGGTATCCTCCTGAGAGGCACCCATATGTGGGGTTCACACCTCCACCAGTCATCCTGCTGGAGCACACCCATTACGGGTCACCTTCTAGGGACACTACGAGAGCCACTATGGCCTCCATATTTGCCTGGAGTGGGAACAGAAGGCAGTGGGGCAGGGGGAAGGAGTCAGGGGCTGGGTGGGGACCGCCGGCTCCTGCAGTTTCTCATGATTTTTCTCTCCAAG
Seq C2 exon
GGCCTTCAAGGAGAGCGAGGTCTCACGGGCCTGACTGGAGACAAGGGGGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636:ENST00000373672:49
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(20.3=100),PF0139113=Collagen=PU(15.7=73.3)
A:
NA
C2:
PF0139113=Collagen=PD(13.0=50.0),PF0139113=Collagen=FE(24.3=100)
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
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development