HsaINT0038683 @ hg38
Intron Retention
Gene
ENSG00000188517 | COL25A1
Description
collagen type XXV alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:18603]
Coordinates
chr4:109301723-109302643:-
Coord C1 exon
chr4:109302169-109302643
Coord A exon
chr4:109302076-109302168
Coord C2 exon
chr4:109301723-109302075
Length
93 bp
Sequences
Splice sites
5' ss Seq
GGGGTCCGT
5' ss Score
-0.2
3' ss Seq
ACCTTTTTCTTTCCTTTTAGGAT
3' ss Score
14.55
Exon sequences
Seq C1 exon
CCGCGACTTCGGCTTCGCGAGTAGCATTGGTTCCTTGGGTTTATTTCGTTTTCCTCTCTCTTCTCCACCTTAGTCGCCCCTTTCGCGCTGCGCTGTAGCGTGCTCTCACAGCCTTTTTGCCTTGAACTGAATGCAGGTGGGAAACAGGTCGGCGTGCCGAAAGACACCGAGTAGGTAGAAATAAGGCAAACTCACAGAGGCGCAACAGGTCCGGTCCTCCGTGGCCAGGGCGAGCCGCGGCCCCGCGTGGCGCCTCGGCCGTTGCCCTCGGACCCTGAGCGGCCACTGTTGGGGCCCTCGAAAGAGGTGTCGGTCCTCTGGGAGTCGGAAGAGCTGTCTGGGTGGGTTTCGTCTTGCTTTTTACCCCACCGCCACCCAGTCCCCGGACGGAGGGTGCTTTTCACTTCCAGCTGGGAGGAGAGAAGAAAGCGGGGATGGTGCACGCCTGCGGGTCTGGACGCTGAGCAAGGCAGGG
Seq A exon
GTCCGTATCCGCTCGTGGGCTTGACTCCACCAACTAGTTGTGCAGCCACAGGGACTGAACTTTGGAGGAATCGACCTTTTTCTTTCCTTTTAG
Seq C2 exon
GATTATTTGAGGTGTAGAGGGTGGGAAGCGAAGCCGAGACGGCCGACCCCGCCACGATGCTGCTGAAGAAGCACGCAGGGAAAGGAGGGGGCCGGGAGCCCAGATCCGAGGACCCGACCCCTGCCGAACAGCATTGTGCCCGGACCATGCCCCCGTGTGCCGTCCTGGCGGCCCTCCTGTCAGTGGTGGCCGTGGTGTCTTGCCTGTACCTGGGTGTGAAAACCAACGACCTCCAGGCGAGGATCGCCGCTCTCGAATCCGCCAAAGGGGCCCCTTCCATTCATCTGCTGCCTGATACCCTGGATCACCTCAAGACTATGGTGCAAGAGAAAGTGGAGCGACTTCTGGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188517:ENST00000399132:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.543
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGTGCTTTTCACTTCCAGCT
R:
TTTCCCTGCGTGCTTCTTCAG
Band lengths:
167-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development