HsaINT0038683 @ hg19
Intron Retention
Gene
ENSG00000188517 | COL25A1
Description
collagen, type XXV, alpha 1 [Source:HGNC Symbol;Acc:18603]
Coordinates
chr4:110222879-110223799:-
Coord C1 exon
chr4:110223325-110223799
Coord A exon
chr4:110223232-110223324
Coord C2 exon
chr4:110222879-110223231
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-COL25A1:NM_032518:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.472
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0139113=Collagen=PU(10.4=20.8)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
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
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)