HsaINT0038616 @ hg19
Intron Retention
Gene
ENSG00000050767 | COL23A1
Description
collagen, type XXIII, alpha 1 [Source:HGNC Symbol;Acc:22990]
Coordinates
chr5:177664617-177666180:-
Coord C1 exon
chr5:177666142-177666180
Coord A exon
chr5:177665702-177666141
Coord C2 exon
chr5:177664617-177665701
Length
440 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCG
5' ss Score
9.67
3' ss Seq
GTCTCTTCCTCCTTTTCCAGTGA
3' ss Score
10.7
Exon sequences
Seq C1 exon
GGCCCCGACGGGCTGCCTGTGCCTGGCTGCTGGCATAAG
Seq A exon
GTACCGTGCAGGGAAGTCTCCAGGGCAGGCTTGGGAGAGGCAGGGGAGGGTGGGGGAATGGGAGGGCCCCAGAGCCTGGGTGCTGTCACTCAAACCTCTGGGTGTCTGCGGCTTCTCGCACAGTGACTGAATAGCCAGGTTTCCCATCATGACCCTGGTTTTGACTCTCCCATCTTGCATGTGAGGCGTGGGGCTGTGGTCCTGGGTGATGGTGTATAACCCATCCTGTGGGTCACATGGACTCAACTGACACCTGGACCAGGCAGGGCAAAGCCATCAGTGCCCCCTGGGATATTGTCCCAACTGGCCCACTGAGAGGGAGTGGGGGGAGGGAAGATAGGAGGAAATGGGCAGGACCGGGGAGGCCAGGCAAGGTGGCCTGGATGGGGGCGGAGCTTCTCGGGCTCCTCGTCACCTTCAGTCTCTTCCTCCTTTTCCAG
Seq C2 exon
TGACCCACAGGCCCAGCTCACACCTGTACAGATCCGTGTGGACATTTTTAATTTTTGTAAAAACAAAACAGTAATATATTGATCTTTTTTCATGGAATGCGCTACCTGTGGCCTTTTAACATTCAAGAGTATGCCCACCCAGCCCCAAAGCCACCGGCATGTGAAGCTGCCGGAAAGTGGACAGGCCAGACCAGGGAGATGTGTACCTGAGGGGCACCCTTGGGCCTGGGCTTTCCCAGGAAGGAGATGAAGGTAGAAGCACCTGGCTCGGGCAAGGCTAGAAAGATGCTACGTTGGGCCTTCAGTCACCTGATCAGCAGAGAGACTCTCAGCTGTGGTACTGCCCTGTAAGAACCTGCCCCCGCAAAACTCTGGAGTCCCTGGGACACACCCTATCCAAGAAGACCCAGGGGTGGAACAGCGGCTGCTGTTGCTCCTGGCCTCATCAGCCTCCAAACTCAACCACAACCAGCTGCCTCTGCAGTTGGACAAGACTTGGCCCCCGGACAAGACTCGCCCAGCACTTGCGGCTGGGCCCGGGGAGCAGTGAGTGGAAATCCCCCACGAGGGTCTAGCTCTACCACATTCAGGAGGCCTCAGGAGGCCAGCCTGCCATGAGAGCACATGTCCTCTGGCCAGGAGTAGTGGCTGAGCTCTGTGATCGCTGTGATGTGGACCCAGCTCCAGGGAGCAGAGTGTCGAGGATGGAGGGGCCCAGCCTGGACTGACTGCTACTTCCTGTCTCTGTTTCCATTATCACCCAGAGAGGGACAAGATAGGACATGGCCTGGACCAGGGAGGCAGGCCTCCCACTCAGAGTCTGGGTCTCACTGGCCCCAAGTCTCCCACCCAGAACTCTGGCCAAAAATGGCTCTCTAGGTGGGCTGTGCAGGCAAAGCAAAGCTCAGGGCTGGTTCCCAGCTGGCCTGAGCAGGGGGCCTGCCACCAGACCCACCCACGCTCTGACGAGAGGCTTTTCCACCTCCAGCAAGTGTTCCCAGCAACCAGCTCCATCCTGGCTGCTTGCCTTCCATTTCCGTGTAGATGGAGATCACTGTGTGTAATAAACCACAAGTGCGTGTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050767-COL23A1:NM_173465:28
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=NA
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(5.7=30.8)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
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)