HsaINT0119635 @ hg38
Intron Retention
Gene
ENSG00000006712 | PAF1
Description
PAF1 homolog, Paf1/RNA polymerase II complex component [Source:HGNC Symbol;Acc:HGNC:25459]
Coordinates
chr19:39389640-39390161:-
Coord C1 exon
chr19:39390069-39390161
Coord A exon
chr19:39389762-39390068
Coord C2 exon
chr19:39389640-39389761
Length
307 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
ATAGGTGTTTCCCCACCCAGGTT
3' ss Score
6.52
Exon sequences
Seq C1 exon
GTCTGGAGTGGTCTGCCGAGTCAAGTACTGCAATAGCCTCCCTGATATCCCCTTCGACCCCAAGTTCATCACCTACCCCTTCGACCAGAACAG
Seq A exon
GTGAGACTAAGGAATGGGAAAACTACTCAGGTATGAGTTCCTTGAAGGCAGGGACTGCTTGTCTCGTTGGCTGCTGTCTGCTCAGGGCCTAGCACAGTACCTACCCTAGCACATAGTAGTAGCTGCTCAATTGTTAATGGAGCAAGCAGTGTCCAAGTCCCTTCCCACTGGGGAGCCAGCTTTCAGACTCTGCCATGGGGGACACTTCATTCTGAGTTCCTCCCCAGAGAAGCTCCGCCTCTGGGAAGCAGGGCTGTGAGGGGTGAAGCTGGAATCCAAACACCACAATAGGTGTTTCCCCACCCAG
Seq C2 exon
GTTCGTCCAGTACAAAGCCACTTCCTTGGAGAAACAGCACAAACATGACCTCCTGACTGAGCCAGACCTGGGGGTCACCATCGATCTCATCAATCCTGACACCTACCGCATCGACCCCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000006712:ENST00000221265:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.156 A=NA C2=0.103
Domain overlap (PFAM):
C1:
PF039858=Paf1=PU(7.1=93.8)
A:
NA
C2:
PF039858=Paf1=FE(11.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
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:
TCTGGAGTGGTCTGCCGAG
R:
CATTGGGGTCGATGCGGTAG
Band lengths:
214-521
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