HsaINT0142377 @ hg19
Intron Retention
Gene
ENSG00000005175 | RPAP3
Description
RNA polymerase II associated protein 3 [Source:HGNC Symbol;Acc:26151]
Coordinates
chr12:48095247-48096629:-
Coord C1 exon
chr12:48096471-48096629
Coord A exon
chr12:48095388-48096470
Coord C2 exon
chr12:48095247-48095387
Length
1083 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
GTTTTTTTTTCCCTCCTTAGAAT
3' ss Score
11.01
Exon sequences
Seq C1 exon
ACCATAATGACTTCAGCAAATAAAGCAATCGAATTACAACTACAAGTGAAACAAAATGCAGAAGAATTACAAGACTTTATGCGGGATTTAGAAAACTGGGAAAAAGACATTAAACAAAAGGATATGGAACTAAGAAGACAGAATGGTGTTCCTGAAGAG
Seq A exon
GTAAATTAAGAATTCGTAATTAAGATCCACCAAAACTAATTTTATAAAAATAAAGCATAACTTTTAAAAATGTTTTGTGAAAATACTGAAATTGAAGTGACTTGCTTCACTGTCAATTTTCTTTTCTTTTTTTTTGTGATGGAGTCTTGCTCTGTCACCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCTGGGTTCAAGCAGTTCTCCTGCCTTAGCCTCCTGAGTAACTGGGACTACAGGCGTGCACCACCACGCCCAGCTACTTTTTGTATTTTTTTTTTTTTAGTAGAGACGGGGTCTCATCATGTTGGCCAGGATGGTCTTGATCTGTTGACCTCAAGTGATCCACCCACCTCGGCCTCCCGAAGTGCTGGGATTACAGGCATGAGCCACCGTGCCCGGCCCACTGTCAGTGTTTTTAGAAATTCTGCTTTTCAAAAAGTCTTTGTAATAATTAAATATATTACCATATTTTAAGGCTTAGTGAGTAGTTACTGAAGGGATGATCATGTGATAATACTTAGAGGTAAATAAATGACTAGCATCATAAAATATGTAGAGGTGTGTGTGTATAAAAATAATATGTGTAGTTATATACTAATGATATATTAACATACCATATTGGCATAAAAATGCAGATAGTACCTAGGTTCAACCAAAAGTTTTTCTTAAGACTGCATTTAAATATGGCTGGGTTTTTCATACTGTACATAATATGGAGGCAGTTCAGTTTGTCTTTGCACTACTGCTGGTTCATCGTACTAAGGCTGAAGATAGGTCGTTTTTGAAGTTTGAATTTAGGATTGCAAATTAAAGGTATAATTAGAATTTCTAGGTAATACTTTTTTCTTGTGATTGAACAATGTTCAACACTCATCAAAGTATGAATTAAACTTTTAAAGTATAATTGTTATAAGTGAAGGTGGTAAATTGGTCTTTTTAAACACTTTAAAATTAAAAAATTCTTAGAAGAAAATATAGTGAGAATTTTAAACATAGCTAGTTATACAAAGAGTAACAGAGCATAATACTCACAACTTTGTGTTTTTTTTTCCCTCCTTAG
Seq C2 exon
AATTTACCTCCTATTCGAAATGGGAATTTTAGGAAAAAGAAGAAAGGCAAAGCTAAAGAGTCTTCCAAAAAAACCAGAGAGGAAAACACAAAAAACAGGATAAAATCTTATGATTATGAGGCATGGGCAAAACTTGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000005175-RPAP3:NM_001146075:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.745 A=NA C2=0.660
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGACTTCAGCAAATAAAGCAATCGA
R:
CACATCAAGTTTTGCCCATGCC
Band lengths:
294-1377
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)