HsaINT0131464 @ hg19
Intron Retention
Gene
ENSG00000138738 | PRDM5
Description
PR domain containing 5 [Source:HGNC Symbol;Acc:9349]
Coordinates
chr4:121737608-121738079:-
Coord C1 exon
chr4:121737987-121738079
Coord A exon
chr4:121737730-121737986
Coord C2 exon
chr4:121737608-121737729
Length
257 bp
Sequences
Splice sites
5' ss Seq
GAGGTTTTG
5' ss Score
-0.23
3' ss Seq
CTTTGCTGGTTGTCTTGTAGTTT
3' ss Score
8.04
Exon sequences
Seq C1 exon
TGTTCTTCAGTGCACAGCGAAAAGCAGTCTAAAGGAGTCTTCGCGAAGTTTTCAGTGCTCTGTTTGCAATTCTTCCTTCAGTTCAGCATCGAG
Seq A exon
GTTTTGTGTCTGAGTTATGAAATGGCTGTTATATAATTGTGGGTCATTTTTTGCATGCATACTTTCATGCTTCTTAGTAATTCAGTTTCACATACCTACAGAATTTAAATGCTTTTCTTCTTACCTGCATAGGTAATGCATGGAATGACCCCGAAACTCTACTAGGGAGCATGTATTACAAAATCTTGCTGATGTTTGAGTTTTGTAGGTATGTCTTCACCATTTCTTCCTGTTCCGCTTTGCTGGTTGTCTTGTAG
Seq C2 exon
TTTTGAGCAGCACCAGGAGACTTGCCGGGGGGATGCCAGGTTTGTGTGCAAGGCTGACAGCTGTGGAAAGAGGCTGAAGAGCAAGGATGCCCTGAAAAGACACCAGGAAAATGTCCACACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138738-PRDM5:NM_018699:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.119
Domain overlap (PFAM):
C1:
PF100834=DUF2321=PD(27.7=71.9),PF047079=PRELI=FE(32.6=100),PF0009621=zf-C2H2=PD(17.4=12.5),PF128742=zf-met=PU(66.7=43.8)
A:
NA
C2:
PF047079=PRELI=PD(11.6=26.8),PF128742=zf-met=PD(28.6=14.6),PF0009621=zf-C2H2=WD(100=63.4)
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:
TGTTCTTCAGTGCACAGCGAA
R:
AGTGTGGACATTTTCCTGGTGT
Band lengths:
214-471
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)