HsaINT0131496 @ hg19
Intron Retention
Gene
ENSG00000164256 | PRDM9
Description
PR domain containing 9 [Source:HGNC Symbol;Acc:13994]
Coordinates
chr5:23522723-23523467:+
Coord C1 exon
chr5:23522723-23522994
Coord A exon
chr5:23522995-23523399
Coord C2 exon
chr5:23523400-23523467
Length
405 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
CTTGTTTTTCTGAAACTCAGATC
3' ss Score
5.48
Exon sequences
Seq C1 exon
ATTGTGAGATGTGTCAGAACTTCTTCATTGACAGCTGTGCTGCCCATGGGCCCCCTACATTTGTAAAGGACAGTGCAGTGGACAAGGGGCACCCCAACCGTTCAGCCCTCAGTCTGCCCCCAGGGCTGAGAATTGGGCCATCAGGCATCCCTCAGGCTGGGCTTGGAGTATGGAATGAGGCATCTGATCTGCCGCTGGGTCTGCACTTTGGCCCTTATGAGGGCCGAATTACAGAAGACGAAGAGGCAGCCAACAATGGATACTCCTGGCTG
Seq A exon
GTAAGAAGAGCCTGCCATTTCCCCTGTTCTGTCTTCCCACATCCCTTCTGTGCCTTTGGTGGGGCATAATCTTCTACATGTTAGTATATAGGTAAGGATAACATGGTTAGCTCTGTGTACTCAAGGTTCTTTGCATGAACACGGAACTCCTATTTAGAGATCAGAGGTTACATGGGAGCAGAGTGGTACAAAGACAAAGAAGTGCATCCTCCCTGTGGAGCTTCTGCTCTGATTGGACAAACCAACTCAGATGTGTAGATAGATGATGACTAAGGTGCATACCATGTGGTCTCAATTGGCAGCTGAAGCTATGCAGGCCCAAAGGCCATTGACGACAGTGGAGTAAAATAATTCTTCTGATTTTTACCCTCTAAAAAGCCTTTGCCTTGTTTTTCTGAAACTCAG
Seq C2 exon
ATCACCAAGGGGAGAAACTGCTATGAGTATGTGGATGGAAAAGATAAATCCTGGGCCAACTGGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164256-PRDM9:NM_020227:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.168 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0085623=SET=PU(16.7=14.3)
A:
NA
C2:
PF0085623=SET=FE(28.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGAGATGTGTCAGAACTTCTTCA
R:
CATCCAGTTGGCCCAGGATTT
Band lengths:
336-741
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
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)