HsaINT0038568 @ hg19
Intron Retention
Gene
ENSG00000169436 | COL22A1
Description
collagen, type XXII, alpha 1 [Source:HGNC Symbol;Acc:22989]
Coordinates
chr8:139674273-139675983:-
Coord C1 exon
chr8:139675948-139675983
Coord A exon
chr8:139674327-139675947
Coord C2 exon
chr8:139674273-139674326
Length
1621 bp
Sequences
Splice sites
5' ss Seq
CCGGTACAG
5' ss Score
5.65
3' ss Seq
CTTCTTTTCTTTTTCTTCAGGGA
3' ss Score
11.71
Exon sequences
Seq C1 exon
GGCCCTTCCGGACCACCAGGAGACAAAGGATCCCCG
Seq A exon
GTACAGTATGCTTTAAATAAAGGGATGAGTTTCTATGGGAGGAATCCTGCTCGAATCAAAGCAGTTTTAAATGGGAAGCACCAAAAACTGAAGTAGATTCTGAAATTTCCTCCTATTATTGAACAGTGCAGACTGTCCAACCTATGAACTCTGACCTGTGGAATACAGTGTGATAGATGTACATATGAGCAGAGAAGGGATGCCACACCCATATTATAGTCAGGCAAACAGACTGGCTTCAGTTTTGGGCATCTTTTCAACACAGAAGGGTGGCCATGGTTTAATGAATTCAGCCAAATTGCCTGAAGAACTAATTTTGAATCCTGGTTTCACCAATCCCAACCACACAGCAGTGAGCCAACATGGGGATTGCTCTTAATCTGTAACATAGGCAGAGCAAGACCCGGGAGCCACTGTGGAGACCTGGTGGACTGACTTCATGCTGAAGCAACAGGAGGGCTCTCAGTCAGCCTTCATTCTTAGGAGCAGCAACCATCCATGACATGCCTGTGCGTGCATTTACTGGGAAAATGCGATTTCCTATAAATTCACCCCAGGGGAAATAGCTGCATTGTAGCAAGTGGGATGATATTGTATCTTATGCCATGTGAACGTATTTTAAATAACCTTTATTTATATGATTTCTGAATTCAGGACAGGGATTGCTTTGTGTGTGTGTGTGTGTGTGAGTGACAGAGTCCTGCTCTGTCAACCAGGCTGGAGTACAGTGGCACGACCTTGGCTCACTGCAATCTCCGCCTCCTGGGTTCAAGCAATCCTCCTGCCTCGCCCTCCCCGGTAGCTGGAATTACAGGTGGGAGCCACCATGCCCAGCACAGGGCTACAGGGCTCCTTATACCCATTTTTATAGATGAAGAAATTGAGGCACTACGTAGTGAACTGATAGACGTGAGATTTCAGAGCAAGTTATGGCAAAGTAGAGGCAAGACAGGTGGGACTCTAGATGGAGGGGTCATGTGAGAGGAGGTCTGTGAAGGCCCAGGAGATGCAGGGTCAGCTCCTGAGCAGCCCGGTAGCACAGTTCCAGCAACTGCCAGGAATTCCCACTTTTAGACCAACTTAAGGAAAAATCTTACGGGAAATGAGATCCATAATGAAAGATATCTGTGCCGTTTCCTGATGTTGTCCAGAAAATTGCAGCTAGAAATTATTTTCTTACAAAGAGTTGTAATCGCCAGGCATATGCTGAGTGTTGTGCTGGGTCTTGCACAAGGAAACTTCTTTAACCACCTAGTTAGAGCTCTCGGGGCTGGTTATCCATAGGACATGAAAGGAGTGAGCCAGGGTTTGAGCTCAGGCCCATCTCACCACAGGAGCTGTCTCTTTCACTCAAGCAAGGGAACTATACAAATGGGGTCCAAGTTGTCAGGCTCAAAATGAAGATTTTCCAGAGCATTCTCTCTGTGTGTCGAGCACATACCTCCATAGGGTACAGTCAGTTGAGTAAGCTCTGAGCAGGGTGCTTTGGCACACATGTTGCATCAGATTCCTCATAGCAACAGACCATGTGTTGAAGGAGAGCCAACTATTGCCAAGGAGGGTGTGTCCTTATTTGCTTAAATATTGTAGGGTGTCAGTGTCTTCTTTTCTTTTTCTTCAG
Seq C2 exon
GGATCACGAGGCTTACCTGGATTCCCTGGCCCCCAGGGCCCAGCCGGCCGGGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169436-COL22A1:NM_152888:42
Average complexity
IR-S
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(19.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(29.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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)