HsaINT0131489 @ hg19
Intron Retention
Gene
ENSG00000164256 | PRDM9
Description
PR domain containing 9 [Source:HGNC Symbol;Acc:13994]
Coordinates
chr5:23507724-23509211:+
Coord C1 exon
chr5:23507724-23507821
Coord A exon
chr5:23507822-23509058
Coord C2 exon
chr5:23509059-23509211
Length
1237 bp
Sequences
Splice sites
5' ss Seq
CTTGTAAAC
5' ss Score
-4.37
3' ss Seq
AGCACCTTCTCCTTCCACAGGAG
3' ss Score
9.58
Exon sequences
Seq C1 exon
CTCTGAGAGAACGCCCGGCCAGGGTGAACGCCGCGGCAGGAGAGCACGGGAGATTGTGAAGAGCATGGGGAGCCTTTGTCGTGCAGCGTGAAACCCTT
Seq A exon
GTAAACCCTCATCCCGAGACCTTCAAATTTTAGCTTGGGAGACCCCAGATCCCCTCACCCTGGGAAGCTCCAAATCCTCTCAGCCTCAAGAGACCCCAAATCCTGCCACCTTGAGGGATTTAAAATCCCCTCAGCATGAAACCCCCAAAGTACCTCAGCTTCAGAGACTCCAAATCCCTTCACCCAGAGGAACAGCGAATCTCCTAATGCTTAGAGCACCAAATATTCTGAGCCTGAGAAGCCGCAATTCCCCTCACCCTAAGGCAACCCAAATCCCTCAGCCTGAGGAACCCTAAATATCTCACCCACAGACAGACCAAATTTCCCCAACCTCAGATAACCTAAATAGCCTGAAAACTCAATCCCTTCAGCTTCAAGGACCAAATAACCTCAGTGTCAAAGACCCTAAAACCCCTTAATGAGAGATCCAAATCTCCTTTACCTGAGACCCAGAATTTCCTCAGCCTCAAAGATCTCAAATCCTTTCATCCTGAGGAACCCCAAATCCCCTTAACCTGATGAATCTCAAATCCTGTCAGCTTGAGCACTCCAAATCTCTTCAGCTTAAAAGACCCCAAATCTCATCCTGAAAAAACCACAGATACTATCAGCCTGAGGGATACCAAAGCTCCTCAGCTCGAGATACCCCAAATTTCCTCAACCTGAAAAACCCCAATTTCTTCAGTCTAAGACATCTCAAATCCCCTCAGCCTGAGGGACCCCAAATCTCAACCTGAGAAATAGCTTCCCCTTAGAGATGCAGACTGCTTTACTCCTGGATTTTTCTAGAATCCTCAGGTAGAGGTCCCCAAATCCTGTCTATGCGAAATGTTCATTTTGTCTCGCTGAAACAGAACTCTGCCCCTCAGTCTGACCCAAGTCTCAGCAGTCGGGGGGCCTCAAGGTCTCCTTGGGACTCCTCTGGCTCTCACACCTCAGGACTCCCCTCAAACACCGGTAGCTACAACCCTCCAGGCACCTGTGCCACCCTTCTCCAAATGAGCCTAGCTGCAGGGGAACTAAAAGAACAAAATCCAGCTTACATTAGGTGGTAGCTCATGGCCAGTGGAGGCCTTCCCATCCCATCAGTACCCTCAAATCTCCCTGGGGTGCTCGAGACCTCACCAGGAATCCACATCTTCCTGCTCTGAACACCCAGCCAGATGGAGAAGACAGAGCCTGGTTCTGGGTAGTGCTCAGGGCTGTTGCCCCCTCTCAGCACCTTCTCCTTCCACAG
Seq C2 exon
GAGCCTTTGGCCTAGGAGCTGGGAGACTCAGGGCCCTTCTCACACTCAGAATTGGAGCAGGGCCTTCTAGACAGTCCCAGCACCATGAGCCCTGAAAAGTCCCAAGAGGAGAGCCCAGAAGAAGACACAGAGAGAACAGAGCGGAAGCCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164256-PRDM9:NM_020227:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=1.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion 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:
CTCTGAGAGAACGCCCGGC
R:
GCTTCCGCTCTGTTCTCTCTG
Band lengths:
246-1483
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)