HsaINT0131463 @ hg38
Intron Retention
Gene
ENSG00000138738 | PRDM5
Description
PR/SET domain 5 [Source:HGNC Symbol;Acc:HGNC:9349]
Coordinates
chr4:120816832-120818527:-
Coord C1 exon
chr4:120818353-120818527
Coord A exon
chr4:120816925-120818352
Coord C2 exon
chr4:120816832-120816924
Length
1428 bp
Sequences
Splice sites
5' ss Seq
ACAGTGCGT
5' ss Score
5.66
3' ss Seq
TTTTTCCTATTTCCCTTTAGTGT
3' ss Score
10.89
Exon sequences
Seq C1 exon
ATCGCCTTGGCTGTAAAGAGGACTATGCTTGTCCTCAATGTGAATCGAGTTTTACCAGTGAGGATATTCTTGCTGAGCATCTCCAGACATTGCACCAGAAACCCACAGAGGAGAAAGAATTTAAGTGCAAGAACTGTGGGAAGAAATTCCCAGTTAAGCAGGCTTTGCAAAGACA
Seq A exon
GTGCGTATATTAAAGAAATATCTTTAAAATTATAAGCTAACACAGTTTATTCCATTCAGCTTAACTCATAGTTTTTAACCTGTGTGTGTGTGTGTGCACGCGCGCACGCGCATGTTTTGTGTGTGAATGAGAGATTAAGCATTTTACATTGGTATTGTCATTAACTCATCTTTTCTTAGTATAGTATGTTGATTATTAAAATATTCAAATTATGGATTTTAACACATAAACACTGTTTATGGTAATTAGTTTTTGTCCATTTATTAATTTGCCATTATGTATCAAGCTTACTGGTTTAATCTGAAATTCAGATATGCCTACTTTAGTTACTCCTTTGAGGTAACAGACTTTTAGTTGTCTACGTTTTATATTCCTTCTGGAATCTGTTTAAAAAAAAGTTTAAGAAATGGGGAGTTCAAAGTATAAAGAATTCCTGGACATTTTGGGAAGCACTGTTTATTTGAGAGCAACTTTGGAGGAATAATTTAAAGATGCATAGGTCCCAGTTATAACAATATGATTAATTAGATGATCCCACACATAGCTCTGTACCCTTTTTTATTTTAACAATTTATATTAACAACATAAAATTATCTTTATTTAAATATTTTACAGGATCAGAAATTGTTAAAAGTGAGAAAGTAGGTATATGCATTTGTAAAGTTTTATTTTTTTACTCATTAAAGTTTGTAATTTTAATCAGATAATTGAATTTAAGTAATTTAAAAGCATATTTACATATTGGATGCAACTGTAGACTCTCATTGTGTTGAAGCCAATTACTTCCAATATGAAAGTAATGTAAATTGTCCCATCTCATCAACATATCTCTTCTCTTATGTGCTCCCATCCTGCCATTTACTTTCTTTCTCCAACCTTAGCTTCTCATTTTAACAGAATGTTACCTTACTTATGAGCAAGAAATCTTTAACATAGGCTTTAATGTTACATTTTTACATTTTTGTGTTTCATTGAACTAAAATTCTGAAATATGCTACATTTCATACTAAGACTGTATGAATATTATTATATGCATCAACTTTTGCTTATAAAAATTGAGATGAAAATTGTGCTTAAAACTTAATAAATGTTCAGAATATCAAAACTTTTATAATAGCAGGATACTACATATTTAGAAATTCTATTGTACTTCCTTAAAAAACAAGCAAGGACTATATGCTTTTAAATAAATAGATGTTAAGTTGCATTCTGGTTAGCTTTTATTGCATTTAGTATTATATATTTATACAAAAGACACTGCTGAGCAAGAGCTTATAGTTAAGGTACTGCTAAAAATTTAAAAAGGCAAAAGACAATGAAAAAAGGGATCACGAACATGACTTTATTCAGAGTTAGTGTAGTTTCATTTTTGTCTTAGAGTTCCAGTTTTTGTTTTCTTTTCTTTCTCTTTTTCCTATTTCCCTTTAG
Seq C2 exon
TGTTCTTCAGTGCACAGCGAAAAGCAGTCTAAAGGAGTCTTCGCGAAGTTTTCAGTGCTCTGTTTGCAATTCTTCCTTCAGTTCAGCATCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138738:ENST00000264808:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF138941=zf-C2H2_4=WD(100=40.7),PF0009621=zf-C2H2=PU(78.3=30.5)
A:
NA
C2:
PF0009621=zf-C2H2=PD(17.4=12.5),PF0009621=zf-C2H2=PU(60.9=43.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCCTTGGCTGTAAAGAGGAC
R:
TCGATGCTGAACTGAAGGAAGA
Band lengths:
265-1693
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