HsaINT0119631 @ hg19
Intron Retention
Gene
ENSG00000006712 | PAF1
Description
Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25459]
Coordinates
chr19:39877334-39879107:-
Coord C1 exon
chr19:39878979-39879107
Coord A exon
chr19:39877440-39878978
Coord C2 exon
chr19:39877334-39877439
Length
1539 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTC
5' ss Score
7.04
3' ss Seq
CCCAAATTCACCCCCTGCAGGGT
3' ss Score
6.73
Exon sequences
Seq C1 exon
GTATGACTACAAAATTGCTCGGGAGTACAACTGGAACGTGAAGAACAAAGCTAGCAAGGGCTATGAGGAAAACTACTTCTTCATCTTCCGAGAGGGTGACGGGGTTTACTACAATGAGTTGGAAACCAG
Seq A exon
GTACTCAGCACACTCCTATCTGATTAGCCTGGATCTGTGCTTCTTAAGACCCTGGGGCATGCAAGAGCCACCTTGGAGGTCATTTGTACCTAAGAATTTGTCATATGCATTGGTAAACAAGAGCAGCAGATGTCTGGTCATGCACATGAGCTGGACTTGGTTCTAACAGGAGGAGCCAGAAAAAAAATCTTTTTTTTTGAGATGGAGTCTCGCTCTGTTGCCCAGGCCAGAGTGCAGTGGTGTGATCTCAGCCCACTGCAACCTCCGCTTCCTGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGCATCACAGGCGTGTGCCAGCATGGCCAGCTAATTTTTTTTGTATTTTTAATAGAGATGGGGTTTCACCATGCTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCTGCCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCACGCCCAGCCAGAATATCTTAATGCAGGAGACATTTAGAGCCTTTGCGCAAGGCAGAGGGCCAAGTTTCCCAGTATTAGTAACAGACTTCATGTGAAAGTAAACATTGCCAAAGTATGGAGTAATATATAAAATTAGCATGAATGTTTTAAATGAAATGCTTAAACCCATGTTCAAAAATGTGACTCCAAAACTCTTCCCTTATGGCTCAAAGTTTACTGCTATGCCAGCACCTCTGGTGTAGAGTTGGGAAGTCTTGAGTTTCTGTTTAAAGCAGAGATTACAAGAACTGTGACCCCATAGGCCAGGCAGGAAATGTAAAAGAGCAGTGGCTGGTAGCATCTGAGTGACCTGGAGTTCTGGGCAACCATGGAGGGCACTATTCACTTCCAGCCCACTGTTGCTGTGCTGTGGGGCCAGAAATTCCTATCTTCCAAAAGCCCCAAATCCAAATGATTTGACATCTCCTGGTTTCTCAAAGTGTTGGTAACTAACTGACACATACAGTAATGCACTGCATGTTTCAGTCAACAATGGACTGCTTATGGTGGTCCCTTAAGATAGAATACCGTATCTTTACTATACCTTTTCTATGTTTAGATACACAAATACTTACTATTGTATTACAATTGCCTGCAGTATTCAGTACAGTCACATGCTGTACAACCTTGTAGCCTAGGAGCAATAGGCTACACCATTACAGCCTAGGTATGTAGTAGGCTATACTATGTACGTTTGTGTAAGAGTACTGTATGATGTTCACATGATGTATATCTCAGAATGTGTCCCTGTTAAATGGCCCATGCCCGTATTTATGTAAATACACCGTATAACACACACACACAGTGTAGGGCAACCAAACTGGTGCCATGGGAGCCATCCTTCCTTTCCCCTGCCCTCAATACCTTGAGCTTAGCTGCCCTTATTCAATCTGTATTTATTCCCATTTACTCTAAGTATTGATGGGGAACCAAGTCAGACCAGACCCCTCACTGGGGGGCGGGGAAGTGGGAGGTGTGTCTTTAACTGCATCTTCCACTTCTCTCTCCCAAATTCACCCCCTGCAG
Seq C2 exon
GGTCCGCCTTAGTAAGCGCCGGGCCAAGGCTGGGGTTCAGTCAGGCACCAACGCCCTGCTTGTGGTCAAACATCGGGACATGAATGAGAAGGAACTGGAAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000006712-PAF1:NM_019088:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.611
Domain overlap (PFAM):
C1:
PF039858=Paf1=FE(10.2=100)
A:
NA
C2:
PF039858=Paf1=PU(25.5=96.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGACTACAAAATTGCTCGGGAGT
R:
CTGAGCTTCCAGTTCCTTCTCA
Band lengths:
232-1771
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)