HsaINT0038592 @ hg19
Intron Retention
Gene
ENSG00000169436 | COL22A1
Description
collagen, type XXII, alpha 1 [Source:HGNC Symbol;Acc:22989]
Coordinates
chr8:139600478-139603744:-
Coord C1 exon
chr8:139603667-139603744
Coord A exon
chr8:139601684-139603666
Coord C2 exon
chr8:139600478-139601683
Length
1983 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TCTTTTGCTCCTTGGGCCAGGTC
3' ss Score
8.33
Exon sequences
Seq C1 exon
GTGAGCGAGGAGCCAAAGGTGACCCAGGTGCACCTGGAGTTGGCCTCCGAGGCGAGATGGGACCCCCTGGAATCCCAG
Seq A exon
GTATGACTCATTCTGCAGTCTCAGGGGTAGGGTGTGAGCTACCCTGGAGACCCAGCACCCCTGCCCGTGGCCCCACAGGACTCAGCAGTGAGCGGAGAGGAGGGCTTAGGCTCTACAGATGAGGAGGAGACAGAGATCACTCACTTGGTTTCATTAAATATTTCTAAAATACGACCTTCTTGACTTACTAAGAAAACTGTAGTGTATTCTATGAATTGTTGAAGTGTATCCCGCGAGTTTAAAATTTCATGAAATGGTCCTGGGAAAAAAAAATTGACTTGGGCTAAATCAGGAACTGCTGGGGACTGTGTTTCTCTTTCAGACATTTCTGGTGCACATTCACTATTGTAAGTGCTAAGGACTCTCGCATTAAAAAATGTGTCTGTTTTGTTTAACCTAGCACTTTCGAAATTCACTTGAAAGAGAAGTCCTTTTTCTTTCACTATACAGTTGTTAATATCCTTTTAGTATTTCTCAGAATATGTTTTGGGGAATGCTCACCCAGTGGTAGGGTGGTTAGCTGTCCCAGGGCTGAGGATGTTTCTGGGAACAGAGGATTTCAGTTTTAAAGCCAAGACATGACTTGAGAAAACTGGGGCAAGTTGGTCATGCTACCCAGTAGCCATGTTGGAAGATCTCTGCAATGCAGCAATAATCACATTCCAGAATTAGATGTATAGGTAGAAGGTAGAAGAAATTTGACTTTTGAGGCTTCTATTTTTTATTTAACTTTAATTTCTGTGTTTGCCTGAGGTCAAATCTGAATATTGATCTTATAGAGAATTTCGATTTTAGTATTTATACCTTCATGATTTTCCAAATTTTCTAAAGTGGATATTTATTATTATTTTTGTTAGATAAGATAATTAGAAATACATTATTAATATTTATTTTTATGGCTCACCTATTTTCAAATAGCTTACAATATTAAGAATAACTTTTAAAAGAAGGCAATTTCAAATAAAGAGTAAATGGCAGAACAGAAACCATTTAAAAGGAGGAAGTAACTGTACCAATAATTATCCCATTTCAGTGGCTCTTAGCCCAAGGAATGAATAACACTGAGGCCTCAAAACTTGATCTAGGCAGGATTATAGATTAAATAGCTATTACCAAAGCATTAATAGAGTTAGTGAAATATCTACAGATCTTTTTAAGTAAAAAGTTTACTTTGTGTTTATTTTATATGATATTTTCTGATAAGACGATTACTAAGACATAAGAAGGGATGTCACTACTAGGGTTAACCACAAGGCTTAGCACTGACCTTCCGAGTTGCCAAAGGTAAGAAGAAAGATAGGTTGATTATATATGATGTCATGATGCTTACTAAGTGAAAGGATAGAAGTTTGTCTATAGGCAATATTTTCTGGGTCTCAATTTTGGACTATTTTAAGTGTCACTTACTTGCATCCTAGATGTTGTCTTTGGCCATGATTTTACAGAATAGCTTAATGTAATCCAAATATGTGGTTCAAATTTAATGTGTAGATAAAGCTGAGAAAATACAGATTTGGAACAAGTTGGATGTTACACAATGGAATGTCACCAGGTGTCTCTAAGGTCATGTGAATTGGGGCTGAGGGTTAATGATCAGGACTTGGTGTCCACTCTCCACTCAGACTCATTCCCTAGACCCATGTAAGAACCCAGAAGGCCAGGTCTCTCATCTGACTCTTCAGTGGAGAAATATGCCCTACCTGGTCTCAATCTACCCTTGTTTCTTTCTCTCCAGTGGTACCTGGATTACTATCCTAGGTCAAATAGTTAAAGCAACCCCTTCTTCTACATATTGAGGTGCTCCTGCTACCTGGTGTTTATGTGGACCACTCTAGTTGCTCAGAGCTCCCAGACCATGGGGATGCTCTGTCTGAGGACGTTTCAGGTCCTGAGTTCATAGTGAATGGAAGCTGTGAGTTCAGGGCCCATCCCCTCCCAGAAGGATCTTGAACCACCTTCTGTTTCTTTTGCTCCTTGGGCCAG
Seq C2 exon
GTCAACCCGGGGAACCTGGCTATGCTAAAGATGGACTTCCTGGGATCCCTGGCCCTCAAGGGGAGACAGGACCAGCTGGACATCCTGGCCTCCCAGGACCTCCCGGTCCCCCAGGCCAATGTGACCCTTCCCAGTGTGCCTACTTCGCCAGCCTTGCTGCCCGGCCGGGTAATGTGAAGGGTCCCTAAAGGACTCTGGAAAGCCAGAAGACTGCAGTGGATTTCTGAAACTTGAACTCAGAGCCCAGTGGGAAGCCAGAGGTCTTGAAAGACTTCAGCCATGTGTTCCTTTTTTTTTTCTTTCTTTTATCGTTTGCTTTTTGTTTTATTTTCTTGAGAGACCTCAAAATTATTAAATCCAACAGACGCTGCCGGTCGGTCAGATTATTATTAATATTATTGTTGTTGTTAATTATTATTATTATTTCATATGCTGATGCTTTGTGAGTTCTTTTCCACTCCTTTAAAGTTGGGAAAACTTGATTCGTGGGGCAGGAGATTGTTTCTTCATTCTTCTGACAGCCCCCATCTGACGCGTAACTGCCCATTTTAAGGAAACTCTTGGTGCTACAAAACCCTGACCAGACACTTGGCAAATTTACCTCTTTCTTCAAAAGAAAAACTTTAAGAAAATGAGCCAATGGGCTTCATTCTCAGTCATGCCCGGAGATCACCCAGGAGAAATAATACAAACACCACCACTGTCCAGAGAGAGTAAAGAAGCAGAAAGAGAAAGAATTTGCAACCATGAGGAATGTTCCCACCTCCCGACGGGACGTGCATTTGGAAAACACAGAATCAGCCCTCAGGGTGCACTCCAGCCACCTCAGTGCTCTAAGCTCACAGAAGTGAAATAATGTCTGTGGGTTGGCAATGGCTTTGTGGGATCATATGTCTTGGCCAAAGATGGGAAAACCTATGTTGAAGAGGCAGCCCTTGAGTGTTAATTTGTCTTCTAAACTGTGTAAGGCCCCTTCAAGTTCCTCTTGTTGGTTTCAATTATATTAATTATAAAACAAGTGGATGTGGTGACCATCCACTTGTGTTTCCCTAATGATGGGCAGTTGGCCAGGGCACTGACCAGAGCTGGGAAATTTGTATCTCCAAGGCGGCTCTGTCTCTGAAATAAATGGCATCAAGTGCATGTGTGTATGCGACATGCCCTGCCTGAACAGGTGCTCAATAAATCCAAGTTTCCTTCTCTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169436-COL22A1:NM_152888:64
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(23.3=51.9),PF0139113=Collagen=PU(24.1=51.9)
A:
NA
C2:
PF0139113=Collagen=PD(74.1=68.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGAGGAGCCAAAGGTGAC
R:
TTCAAGACCTCTGGCTTCCCA
Band lengths:
342-2325
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)