HsaINT0038185 @ hg19
Intron Retention
Gene
ENSG00000084636 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:2193]
Coordinates
chr1:32140859-32145286:-
Coord C1 exon
chr1:32145233-32145286
Coord A exon
chr1:32140913-32145232
Coord C2 exon
chr1:32140859-32140912
Length
4320 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
GTGTCTCTTCTTGGCTACAGGGA
3' ss Score
7.88
Exon sequences
Seq C1 exon
GGTCCACCAGGTATTCCCGGACCACCAGGCCCCCCTGGAGTACCTGGGCTGCAG
Seq A exon
GTAAAGGGGGAGAAGAGAATGAGGAGCTTGGGTGGCAGAGCTCATGGGTCAGGATGGCTGCTCCCGGCTGGACCCCAAGGATGCTGCTCCCCCACCCCAAAAACACAGACATGCCATTTCTCACTCCTCTGTTTACCTGCCTCCCAGGGTGGCAAGGAGGGCCCACTGAGCCTCTAGGCCAGGCTCTGCACTCCCAGCACTGTTTCAAGCAATGCACTGTTGCGTCAGCTGTCAGGCACCCACAATCTGGGTCAGATAAAAATCCCTTACCCTGGTACAGAGCCCGGCCCACTGTTTTGGAGTAGCATTCAACACTCATTCATGCAACATGTGTTTTTGCACATTTGCTATTTTCTGGCACTGCTTTAACTGCTGTGAATACAGTAGTGGCTAAAAATAAAAGTCCCTGCCCTCTTGGAGCTTATATTCTAGTAAGAGAGACAGACAATAAGCAAGATAAATAAATAAAATATAGTGTGTTAGAAAGTGATACATACTAAGGAGAATGGTAAAGCAGGGAGTGAGTATAGAAAATGGGATGAGGGCAGGAGAAGTATTTGCAAAATGTACTGAAAAGAAGGTGATGTTTGAATCAAAACTTAAAAGAGATGAGAAGCTGTGAGGGATAGCCTTTGTGGCAGAGAAAACAGCCGGTGCAAAGGCCCAGAGGTGGGATGTGTTTGGGGAATTGCAAGGAAGCCAGAGATAGTGAGGGAAGAGCATTAGGAGCCAAGATCTGTGTGACACTGTGAATAAAGGGTACATTCCAGAGGCAGGCAGCCTGAACTTGAATCCCGGCTCTGCCATGTGCTAGCTGTGTGACGGTAGGCAAGTTCCTTAACCTCTCTGTGTCTCACTGCCCTCTTCTGCTAAGTGCGCCTAACTCATAGGGCTTTTGTGAGTATTAAACAAGTTAATGCATGTGAAGGGTATAGAATTGTACCCATGACTATTATATATTATTTATGTGACAAATGCTTAGAAGGCATTAGCTATCATTATTATGATGATGAGTACTATTATTATTTTACGTCCATTCTTTTATTCATTTGAGCCTTACATAAAAGCCCCAAAAGGAAGGCAGTATTATTATTCCTAAGTCACAGCTGGACAAGCTGAGGCTCTGAGCGATGGAGTATCTTGTCTAAGGCCGCCCGACTAGGAATTGACAATGCTAGACTGGGGCTTCCCCATGCAAAGCACTTTTTACCTTCTTCTGATGCCTTTCAGGACAGTTCCCAGTGGTTTGCCTAGCAAGCCACGTTTTCCAGAGGTTCTAGGTGGCATAGACACCACTGTCCGTGTGTCTGGCTCCCAGCTCCTAAGAGAGTGATTCTCACCTGAAGAAGCAGGGCAGCATCACATGGAAGCTTTTTACAAGCTACTCCTCCTTGCCCCAATGATTTGATAGATTTTGTATCTTCCCTCCCCACCCCCGCCACCCTGGCACACCTCCCCTGCCACCGTGGGCTGGGAGTCTGCTCTAGTGAGCCACTGTTGCCGATGGGAGTCTCTGCCAGGATCCCAATTCTCTCTACCCTATTGGAAGTGCTGAACTAGAGCCCACGCCACATATTTGCAGCCACACATTTGCCGAGTGTCTGGGGCTTTTGGGGCTTCCTGCCACACTGCCAGGAAACAGGAATCTGTCTGCAGAGGGCTTGCAGTTTGCTTGGGGAAGTGTAAGAGTCATTTCAAAGTGACCCATTAATAAGCGAGAGCTGATGTAGTGTAAACCCTGCCAAGACATGCTGGGGAATGAGGCAGAAAAGAGTGACTGCTGAGTCTGGTCCCAGGCACCAGAGTCCTTACCTAGTGCCAGTGCTTGAGACCAAGCCGAGGCTGCTGCTCACAGGTACCTGCCCCATGCCAGGTGGGATGCAGGAGGGCCAAGCAGCTCCTTTATTCAGGTATAGAAACAGGCTCAGGGATGTACAGCACTTACTCATCCAAGGCTGTATTGTCCCAGTGCTTAGTTATCTCATTTCATCTCAGTCCATTCCACAGAGGAGGAAGCTGAGGCACTGAGGTTAAGAAAGATGCCTGAGGCAACTAGTAGGTCATTGAGCCCAGCTTTCAATTCTGGCTGCACTTCGCTTCCGCAGTAGGACAACAGGTAGAACATTTAGTTCTGAGAGGTCAGGAAAACAATTACAAAGTATCAGGCTTGAACTATCACACTGGCCCTGGAGAGGGGAGCAAGGGATGAATAATGATTTAAGGCATAATAATTAACATGTTCGGGCCAGGCGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTCGGCAGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAGCATGGCGAAACCCCGTCTCTACTAAAAATACAAAAAGAATTAACCGGGTTTTGTGGTGCATGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAAGCGGAGGTTTCGATGAGCTGAGATTGCACCACTGCACTCCAGCCTGGGCGACAGAGTGATACATCTCAAAAATAATAATAATAATAATAAATAAAAAATAATAATTGACATGTTCAAGGCATTTTCCCTGTGCCAGGCACTGCTCTAAGCCCTGATGGTGCACAGAGGTGCCAGGGGGCCTGGATGGTGGCTGGCTCCGGGTCTGACCCAGGCCTGGTAGAGCCTGCCTGGAAATTGCTCGGGGGCTGGTGATATGTTCCATTGCTGGGAGCTGGGACTTGAAGGAAGGCCAGATCTCAGAGTGCGCCAAGGAAATCCTGTGCAGGGAGGAGCAGGCTGAGCAGCGGTGCATTCACTCAACACGTACTTACTGCACATCTCCTCCATGTTGGGTGCTGGGGATTCAAAATGGAACATACTCCCTGCCTCCATGGAGTATTTAATATGCAAATGTGCCTCACGAATCTGCAAGGGGAACATTGTCCGGGTGGCATGGATTTAATGTAAACATCGTTGCAGCCATTGTCTCCTTGAAGCCTCACCATAAACTATCCCTGTTTTATAGATAAGGCAACTGAGGCATAGAATTTTTTTCCCCCAAATAAATTGCCAAAAGTTATACAGGTAGTCAGAATTTTGTATCTAGATGAATCTGACTGGCAAGTACCCACCCTTGCTGTGTACATGAATGTTCTGGGGATGTCTGTTGAGGAATGATGCTAGAATTGTGGTTAAGAGAGGGGTTAGAAGCCAGTGATCCTTGCTCTGGACCTCAGCTCTGTGCCTTGCTCAACTTGTGACCTTTGGCAAGTTACTTACTCCTCTGGGTTCTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCCCTCTGTTGCCTAGACTAAAGTGTAGTGGCGTAATCTTGGCTCACTGCAACCTCCATCTCCCAGGTTCAAGTGATTCTCCTGTCTCAGCCTCCCGTGTATCTGGGACCACAGGCACACACCACCATGCCCTGCTAACTTTTATATTTTTAGAAGAGACGGGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAATTCCCGGCCTCAGGTGATCCGCCCACCTCGGCCTCCCAAAGTGCTACGATTGCAGGTGTGAGTGACCGTGCCCAGCCTCCTCTGGGTTCTTTGTGCTATTTTTAAGATGGAGATAACAGCACCTAGTTCAACAAGATAGCTGTGATGATTAAACGAGAAAATAGGCTGGGTGTGGTGGTTCACGCCTATAATTTCAACATTTTGAGAGGCTGAGCGGGGAGGATCACTTAAGCCCAGAAGTTTGAGACCAGCCTACCAGCGAGACCTGGTCTCTATAATAAACACAAAAGAATTAGCCAGGCATGGTGGTGAGCGCCTCTAGTCCCAGCTACTCAGGAGGCTGAGGTGGGAGAATCGCTTGAGCTGAGTTTGAGGCTACAGTGAGCTATAATTATGCCATTGCACTCCAGCCTGGGTGACAGAGTGAGACCCCGTCTCTACAAAGAAAAAAAGAAAAAAGAAAAGGAAAGGAAAAAGAAAGAGAGAAAATATAGAAAAACGACTTAGCACAGAAATAAACAGTAGTTCCATGGAAGACCCTCTGCTCAATTTCTGACCTTCCCTCTGATGTGGGGGGAAAACACTTGCTGTTGGACGGTTTGGGGGGTCGCTCTTCTGGGCCTCCCTGGCTTTCCCTATAAGGGTCGAGAGGCTTTTGAGCTAAGAATAGATGTCAGCCTTGTGCCAGCCAGGGCTCTCAGCTCTGCAGGACAAGGGGAAGAGGAGGCGGGGATGATGAGAAGGAAACAGGCTGACCAGCAGGCTAGAGAGATGGAGCCCACTCACTCGTGTCTCTTCTTGGCTACAG
Seq C2 exon
GGAGTGCCTGGAAACAACGGTTTGCCAGGACAGCCTGGGCTCACTGCAGAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636-COL16A1:NM_001856:42
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.914 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.0=100)
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
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)