HsaINT0131494 @ hg19
Intron Retention
Gene
ENSG00000164256 | PRDM9
Description
PR domain containing 9 [Source:HGNC Symbol;Acc:13994]
Coordinates
chr5:23521132-23522514:+
Coord C1 exon
chr5:23521132-23521288
Coord A exon
chr5:23521289-23522412
Coord C2 exon
chr5:23522413-23522514
Length
1124 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
TCTACTCTTCTCCAACCTAGAAC
3' ss Score
7
Exon sequences
Seq C1 exon
GGAATGCCCAAGGCGTCATTCAGTAATGAATCTAGTTTGAAAGAATTGTCAAGAACAGCAAATTTACTGAATGCAAGTGGCTCAGAGCAGGCTCAGAAACCAGTGTCCCCTTCTGGAGAAGCAAGTACCTCTGGACAGCACTCAAGACTAAAACTGG
Seq A exon
GTAAGAAAAAATATTTGCGGGGACTTTAGTCCCTCTATGTCCTCTAGAAAGGTTGATGAGTATGGTCTACCTATGTGGGGTGGACTTTGCATAGGCCTGGGCTTAAGCTGGACTCAACTGTGAGACCAGAAGGTAGATGCAGTATTTTGTTAAAATTATTTATTTATTTGTTCACTGAGACAGAGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGTTCACTGCAACCTCTGCCTCCATGAAAATAGATGTTTTCTTGCCTCAGTCACCCGAGTAGCTGGGATTATAGGCGTGCGCCACTGTGCCCGGCTGATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCTTGTTGACCAGGCTGGTCTCAAACTCCTGGCCTCAAGAGATCTGCTCACTTCAGCCTCCCAAAATGCTGGGATTACAGGCTTGAGCCACCATGTCCAGCCTTGGATACAGTATTGAATAGCATGTAAGAACATTAACTTTGAAGTCATTCACTTGGGTTATAATCTACATAGAAGCACTGGGGCCTTGGGCAAATCTTATAAATTCTCTGAGCTCCTGAATGGTAATCTGTAAAATGAGACCAAGTATATATAGACCAAGTACATTGTTTGAAAGCATTAAATTAAATATAAATGAACCCATACATGCAAGGTGTCCAATAAGTACCTCTCTGATAATAGATATTCTTTTGTGCATTTCTACATTTCCTCTTCCATCACATGTCTACTAGTTTGTAGAAGATCCCCTATAGAGATCATACTTTATCTTAGTGTTGTATGTCCAGGCCTTTGTTCAATGCCTAAGATGTAATGTGACCTCAAGAAATATCTTCCAAATGAATAAATGCATGAATGAACCATTTTGTAAGTAGAAATGTTGGGAGGTTAATGGTATAATGAGAACAGCCAGAAACTAATATTAAATAGGCATCTGCAGTCAGTGTGGGTGTGGGGTCTAAGTCTCTCTGAAGCAGTAGTTAAAGAGGGGGACACTAGAGTATGTAGAAAGGTAGATGCCAATTTGATGGTAGATTTCACATTTTCTTATGAAACAAGGACAAACACCCCAGATTCCCAATTTTACCCGTCTACTCTTCTCCAACCTAG
Seq C2 exon
AACTCAGGAAGAAGGAGACTGAAAGAAAGATGTATAGCCTGCGAGAAAGAAAGGGTCATGCATACAAAGAGGTCAGCGAGCCGCAGGATGATGATTACCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164256-PRDM9:NM_020227:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.906 A=NA C2=0.600
Domain overlap (PFAM):
C1:
PF095145=SSXRD=PU(0.1=0.0)
A:
NA
C2:
PF095145=SSXRD=WD(100=94.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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:
GCCCAAGGCGTCATTCAGTAA
R:
AGAGGTAATCATCATCCTGCGG
Band lengths:
254-1378
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)