HsaINT0038616 @ hg38
Intron Retention
Gene
ENSG00000050767 | COL23A1
Description
collagen type XXIII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:22990]
Coordinates
chr5:178237618-178239179:-
Coord C1 exon
chr5:178239141-178239179
Coord A exon
chr5:178238701-178239140
Coord C2 exon
chr5:178237618-178238700
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
TGACCCACAGGCCCAGCTCACACCTGTACAGATCCGTGTGGACATTTTTAATTTTTGTAAAAACAAAACAGTAATATATTGATCTTTTTTCATGGAATGCGCTACCTGTGGCCTTTTAACATTCAAGAGTATGCCCACCCAGCCCCAAAGCCACCGGCATGTGAAGCTGCCGGAAAGTGGACAGGCCAGACCAGGGAGATGTGTACCTGAGGGGCACCCTTGGGCCTGGGCTTTCCCAGGAAGGAGATGAAGGTAGAAGCACCTGGCTCGGGCAAGGCTAGAAAGATGCTACGTTGGGCCTTCAGTCACCTGATCAGCAGAGAGACTCTCAGCTGTGGTACTGCCCTGTAAGAACCTGCCCCCGCAAAACTCTGGAGTCCCTGGGACACACCCTATCCAAGAAGACCCAGGGGTGGAACAGCGGCTGCTGTTGCTCCTGGCCTCATCAGCCTCCAAACTCAACCACAACCAGCTGCCTCTGCAGTTGGACAAGACTTGGCCCCCGGACAAGACTCGCCCAGCACTTGCGGCTGGGCCCGGGGAGCAGTGAGTGGAAATCCCCCACGAGGGTCTAGCTCTACCACATTCAGGAGGCCTCAGGAGGCCAGCCTGCCATGAGAGCACATGTCCTCTGGCCAGGAGTAGTGGCTGAGCTCTGTGATCGCTGTGATGTGGACCCAGCTCCAGGGAGCAGAGTGTCGAGGATGGAGGGGCCCAGCCTGGACTGACTGCTACTTCCTGTCTCTGTTTCCATTATCACCCAGAGAGGGACAAGATAGGACATGGCCTGGACCAGGGAGGCAGGCCTCCCACTCAGAGTCTGGGTCTCACTGGCCCCAAGTCTCCCACCCAGAACTCTGGCCAAAAATGGCTCTCTAGGTGGGCTGTGCAGGCAAAGCAAAGCTCAGGGCTGGTTCCCAGCTGGCCTGAGCAGGGGGCCTGCCACCAGACCCACCCACGCTCTGACGAGAGGCTTTTCCACCTCCAGCAAGTGTTCCCAGCAACCAGCTCCATCCTGGCTGCTTGCCTTCCATTTCCGTGTAGATGGAGATCACTGTGTGTAATAAACCACAAGTGCGTGTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050767:ENST00000390654:28
Average complexity
IR
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
(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