HsaINT0142392 @ hg19
Intron Retention
Gene
ENSG00000005175 | RPAP3
Description
RNA polymerase II associated protein 3 [Source:HGNC Symbol;Acc:26151]
Coordinates
chr12:48073487-48075600:-
Coord C1 exon
chr12:48075479-48075600
Coord A exon
chr12:48073558-48075478
Coord C2 exon
chr12:48073487-48073557
Length
1921 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTTTAAAAAATTCGCTTTAGATT
3' ss Score
5.92
Exon sequences
Seq C1 exon
ATATGAAGAAGCTGAAAAAGACTGCACACAAGCCATTTTATTAGATGGCTCATATTCTAAAGCTTTTGCCAGAAGAGGAACTGCAAGAACATTTTTGGGAAAGCTAAATGAGGCAAAACAAG
Seq A exon
GTAAGACTTTATAACAGCTGGCACTCAGTCATCCTGATGAGTGCCCAAGTTAAAGAAGCAGAGATTCATGTAGCTTACCCATGGTTCAAAGATACTGAACTTAGGGAATTATGTTTTCTTTCCACAGTTTAGATCACGAATAGATTTGGAGGAATGCAGCTTCCGCAATGTACCAGATTATCTTTTTGTTTAGTAGCATTCTGGCTAATTTTGTTTAGTACATTCTGGCTAATTGCCAGTCAATATTAATGAAAAATTTTAATTATACATGAGAATGGAAAACGATAAAAAGACCAGAATGGAAAGGAAGGGAATCGGTGTTGTTGAGCGAAAGGGACTCACTGTGTGATATGCTTGAAGCCAATACTGTGACATCAGGTTTTTGAGAAAAGGCTTTATTTATATTGAAAGTTGACTCCTAAAGAGACAGGAATCAAACCCAAATCTGTCTCCTTGTCCTGGCCTTAAGGCAGTAATTTTATTAGAAAGGGTTTAGGGAGGTGGATACTGGAATTAGCAGGTAATTAGTGGAAGGAAAGGGAAAAGTTCTTGGGCATATGTAGCTATCTCTTCTTGCTAACTAATGGGATTGCAGGTGCAAATTTGGGGTAGTTAGTAGAACTTGGTGGAAATTCAGTTTGTGACATCAGCAAACTCGTTTTTGTGCAAACTCCACTTGGCCATCTTGGTTCCAAATGATTTCAGCCTGTTTTTTTTTTTTTGTTTCGTTTTTTTGTTTTTTTTTGAATCCCAGTAAGCAGAGGAAGTTTCTTTGTTTCAGCAAGTTGTATCTTTTCCTATCTGCCATCCTACAAACTGAAGAATTTCTGTTAGTGATTGATTTTTTTTTTTTAAAAAACTCTTCGGGCTGTGGTTTTATCAGCAGGTAGGGAATGGAGGATAATGGAGATCTGATACCATTTTAATTCTTGATACTATTTTTTTTCTTTGTTTTTATGGTCTTCTCTTTTAGGGTATTCATTGAATTAGTCTTTTCAGAGAACCAACTTGGTTCTCCTGTGTGTGTTTTCTATTTAATTTCCTTCTGCTTTTTATTTTATTCCTTCAACTTTCTTTTGGTTTAATTTGCTGTTTTTCTAGCTTCTTGAGATCAGTACTTAGATAATTGATTTTCAGCCTCTGTTCTTTCCTGGTATGTGCATTTAAAATCTGGCAGTTTCTCTATAAGCCTGTTAGCTACAGCAGTGTTTTTTTTATTGTGGTTAAAAAAAATATGTAACGTTAAATTTATTATTTTAACCATTTTTCAATATATAGCTCAGTGGCATTAAATACATTTACATTGTGCAGCCATCACCACTGTCCATCACCAGAACTTTGTCATCATCCCATTCTAAAACTCTATACACATTAAACAATAACTCTCCATTCTCCTCTCCTCCCAGCCCTAGTAACCTCCATTCTACTTTCTGTCTCTGAATTTGACTGTTCTAGATATCCTATGTAAGTGGAATCATGCAGTATTTGTCCTTTTGCCTCTGCTTATTTAACTTAGCATAATGTCCATGTTGGAGCATATATCAGAATTTCATTCCTTTTTAAGGCTGAGTAATACTTTGTTGTATGTAATTCTCTTATTCTATTAATATTTTACATTTAGTGAGTTACTCTGTCATTTGTTTACATGGTGAACTTTGCTAAGTTAGATGACCTCTAGGGGCCTCAGTTTTATCACCTTTAAAGTGGGGTTGTAGTGAGGGTTACGTGAACATTCATATAAAACAACTACAACAGTGTTCAGTAAATGTTCTTACTATAGCTCACCTGTTTCCTAGTAATCTGAGTAAAACTGCTTGAGCTAAAAATGTGATTACTAACTGAATATATCATGAATATACATGCGAATATGAAAACTCCACATTTTAACTATGTTGTAATGTTTTTAAAAAATTCGCTTTAG
Seq C2 exon
ATTTTGAAACTGTTTTACTTCTGGAACCTGGAAATAAGCAAGCAGTAACTGAACTCTCCAAAATTAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000005175-RPAP3:NM_001146076:9
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=0.010
Domain overlap (PFAM):
C1:
PF134141=TPR_11=PD(23.5=38.1),PF0051523=TPR_1=PU(64.7=52.4)
A:
NA
C2:
PF0051523=TPR_1=PD(32.4=45.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATATGAAGAAGCTGAAAAAGACTGCA
R:
TGGAGAGTTCAGTTACTGCTTGC
Band lengths:
182-2103
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)