HsaINT0132640 @ hg19
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:16463]
Coordinates
chr2:153535866-153537850:-
Coord C1 exon
chr2:153537740-153537850
Coord A exon
chr2:153535987-153537739
Coord C2 exon
chr2:153535866-153535986
Length
1753 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
AACAGTTTTTTCCTTTTCAGCAA
3' ss Score
8.53
Exon sequences
Seq C1 exon
AAATCAATGTGGACTGAACATAAATCACCTGATGGAAGGACTTACTACTACAACACTGAAACCAAACAGTCTACCTGGGAGAAACCAGATGATCTTAAAACACCTGCTGAG
Seq A exon
GTAAAAGTTTGAGAGCTGGAATTCAGGGACTGTCAAGTAGACTGGGGCGTATTTTTTAGGATTCTATAAGTAGTCGATTATCAAAGAGCAGTACTGCTTAAATGTCAGAAGAGGATCTGTAAAGACATTCAGAAAAAAAGAGGGTTAGTATAGTCACACCAATCGGGAAGAAGAGCAATAAAACTCAACAGAATAATTTTATTTACTGATTTTACCCCTGCTTAGAAAACCTAGTAGAGTGGGATCAATTTTAAAAAGGTGATTTAAAGAATAAATTGGAAGTGGGGAAGACTGTTTCTTTGCCTGCCGCTGGCTTTTTTTTCTGATAGCAAAACTGGGTGATTTTAAATGACTTCTACTGAGTTCTTAAATTTCCAGTAGGGTTAAGGGTAGTGGAGATGAAATTAAGTTACCTACAAATACTTCCTTCTCTTAGAGTGGGAAGTTTTCTCTTTGCAGGAAATGCCCTTTTAAAAAGTGTGTTTTTATTTTGTTTTTTGTTACAAGTTTTACCATTCAAAATATACAGATATTGAAGAAAAAGTTAAGGTTGAAGGAATAAACTGAATTAAGCAATGTCACATGTTGTTTAATTAGAAACTCTGGGGTGCTAAGTAAGTAAGAGTTGATCTGGCACTCCAGGCTATGCTTAAGTTTCATCCTAGCTGGTGGTATACCTTTTTGTTTTCTTCTCTTCCTAATTAAGGAATTTGAGAAGGTAAAAGTATTTTCCAGGTTGCTGTACTAACATGAACAGCAGTGCTTGGGAGGGGAGGTCGGACGATTTTTAAAAACATGTATTCCAGTACTGATTTATAGCCAATGATATTAATTACATACTTTGTCCAAGACACTCTGTTTGGATTCACACTTTGAATAGATTTCTCATACTACCCTAACAGGTTTTGTTTATTCGATTTTAAGTATATTATACCTACATGTTTTCTTACATAATAAGTTAATTCGTTCATAAACTACGAAACTGAAATCTAAGCATGACTAAATTAGATTTTGTTTTTTTTGAACTTTTATGGTTTTCCAACTAATATTAGTATCAGAGAAGTCTGTTAAATGTGGATGATAGGCCGGGCGCGGTGGCTCACACTTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGTTCGAGACCACGGTGAAACCCCGTCTCTACTAAAAAAAAATACAAAAAATTAGCTGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCAGAGAGGCTGAGGCAGGAGAATGGCGTGAACCCGAGAGGCGGAGCTTGCAGTGAGCCGAGGTCGAGCTACTGTACTCCAGCCTGGGTGACAAAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAATGTGGATGATAATCTTGACCTATAATGGGGTGTGAATGGTTACAGTAAATAGGATTTGAAATTCATATAGAACTGGTTTTGAATCTTGTCTCTGCTTTTTAATGAGTATATTACCTTAAACAAGTTACTTTCTGACTTCAAGTAACAGTCCCTAGATACAGAATTATGTTACACATTTTGCAGTGTTATAAAGATTAAATAATGTATTCAAATGGCATCACTCAGTGAATATTCAATAATTGATAGTTTATATTATTACCATCATCTCACGAGTTTTAGAATTGTATCAATTGGTAATTTCTAGTGAAAACAGCCATGTAAATGATCAGTGATGTTAAATATATTATTATTAACAAACAGTTTTTTCCTTTTCAG
Seq C2 exon
CAACTCTTATCTAAATGCCCCTGGAAGGAATACAAATCAGATTCTGGAAAGCCTTACTATTATAATTCTCAAACAAAAGAATCTCGCTGGGCCAAACCTAAAGAACTTGAGGATCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504-PRPF40A:NM_017892:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.820 A=NA C2=0.527
Domain overlap (PFAM):
C1:
PF0039721=WW=PD(93.3=75.7)
A:
NA
C2:
PF0039721=WW=WD(100=73.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCAATGTGGACTGAACATAAATCAC
R:
CTTCAAGATCCTCAAGTTCTTTAGGT
Band lengths:
230-1983
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)