HsaINT0131491 @ hg19
Intron Retention
Gene
ENSG00000164256 | PRDM9
Description
PR domain containing 9 [Source:HGNC Symbol;Acc:13994]
Coordinates
chr5:23509579-23510136:+
Coord C1 exon
chr5:23509579-23509702
Coord A exon
chr5:23509703-23510028
Coord C2 exon
chr5:23510029-23510136
Length
326 bp
Sequences
Splice sites
5' ss Seq
TAGGTAACA
5' ss Score
6.25
3' ss Seq
AAATTTTTGCTTCTTTTCAGGTC
3' ss Score
10.78
Exon sequences
Seq C1 exon
GTCAAAGATGCCTTCAAAGACATTTCCATATACTTCACCAAGGAAGAATGGGCAGAGATGGGAGACTGGGAGAAAACTCGCTATAGGAATGTGAAAAGGAACTATAATGCACTGATTACTATAG
Seq A exon
GTAACAGGAAGTGCTGGGCACAGACCAGCCTGGGAGACATAAAACAGGTCTTTGGTCCCTATATTATTTTAGTTCTCAGGTGGTGGCATCTGCCCACAATTCCCTTTTTCATGTAGACAAATCTGGAGGGAAATTTTGTTCTTTTGCGTCAGTGCAGGGCTGAGTGTGGATATTGACCATGCAGAGGTCACATCTTGACCTTGTTCAAGACTCTCCCAGCTCATCAGACTGAGCAGCACTGGCTTTGTGGTGCTTTCCATTGCCACTGCCCTTTGTTCCTTCTCCCAGCTCTTCCATTTTAGAACAAAATTTTTGCTTCTTTTCAG
Seq C2 exon
GTCTCAGAGCCACTCGACCAGCTTTCATGTGTCACCGAAGGCAGGCCATCAAACTCCAGGTGGATGACACAGAAGATTCTGATGAAGAATGGACCCCTAGGCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164256-PRDM9:NM_020227:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.644
Domain overlap (PFAM):
C1:
PF0135222=KRAB=WD(100=92.9),PF0230512=Phage_F=PU(40.9=85.7)
A:
NA
C2:
PF0135222=KRAB=PD(0.1=0.0),PF0230512=Phage_F=PD(47.9=94.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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:
GTCAAAGATGCCTTCAAAGACA
R:
TTGCTGCCTAGGGGTCCATTC
Band lengths:
231-557
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)