HsaINT0132619 @ hg38
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr2:152715995-152717981:-
Coord C1 exon
chr2:152717356-152717981
Coord A exon
chr2:152716127-152717355
Coord C2 exon
chr2:152715995-152716126
Length
1229 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
AAATGTTCACTGTTTTTCAGATG
3' ss Score
8.18
Exon sequences
Seq C1 exon
GATCGAACCCTCTCCTCCGAACCCCTCCTTTCGCCTTCCCCGCCTCCTCCCCTCCGCCTCGAGCACCGCGCGCGCGCATTCGGTCCCAGCCACCGCTAACACTACAGGCTGCTTACCCCCGCCCCCTCCACCCTACCCCTGGCGGCCTCAGGTTTGTGGGGCGTACGTAACTCGGGCGGGGAGGGTGAAGGTGGCAGACCCCCACTGCCCCACCCCCTACGGGGTGAGGCGGTCTAAGCTCGGGAAGCTGGGACACTGTTGTCTTCCCTTCCCCTGGGGAAGTTGGTAGAGTTTTCCCGACGGAGGACTCGGCGCAGAAACTTCCTCCGTCCTCCTCCTCCCCCCCCCCCATGCAGGCGACGCCGAGTGAGGCTGAGGCTGGGGGCGAATCGCCGCAGAGCTGCGTGTCGGCGGCGCATTCTGATTGGACAGCGGGGAAGCCCGTCAGCCTGTTGGCCCCGCTGATCCCGCCCCGTAGCGCAGGGCAGCCTTTAACCTTTAGCCCCAGTGGGCGCCAGCCACTCAGATCGCTTCTTGTTGGTATGTGTAGCGGCAGTGGCCGCCGGCGGAGCAGTCTGAGCCCGACGATGAGGCCGGGGACGGGAGCTGAGCGTGGAGGCCTCATG
Seq A exon
GTGAGTGAAATGGAGAGCCATCCTCCCTCGCAGGGTCCTGGGGACGGGGAGCGGAGATTGTCCGGCTCAAGCCTCTGCTCCGGCTCTTGGGTCTCTGCTGACGGCTTCCTGAGGAGACGGCCCTCGGTAAGGGATCAGTGGGGCAGGGGGAAGGCGGCACAATGAAAAACGGAGTGAGAAACAGGAAGCTTTCTCCGAAAGGAGAAGAAGATAAGAGTGGACGAAGGAAGAACTCGAGATGGTGGGATATGTTCTGAGGGAGAGAAGTGGAGGGTGGAAATGCACAAAGAGAAGGATGTGAGACCCTGGAAGTTCCCCGTGGGCTTGGCCTAGACAGATGCGTGGTGAAGGTGCTGGCTCTTGGGCGGGGTGAGCGTCTTGGAGCTTTAGGCCCGATTTTAGCTGGGAGGGGGAGGCAGGGGCTTGATACTGTAAGACTTTAACAGCGGCTGCCAAAATTTGTTTTCATTAGTCGTCGGGGTGGTCTGCAGGGGGAACTGTTGGGACAATTGGCAGGAGATAATTAGGTGGTTTTAATTTAAAACATAGAACAATGGACTCATCGGTAAAGAAAGTAGTTGTCTTTTTAAACTGCGTTAAAAAGGATGAATTAGTTGTTTGCATTTAGTGTCCGTGAGTGACAGAACCTCAGTCTTTGAAAATGTATTTTTGGCAGAAGGAATTTTACCTGTCTTAAAGGTTATGTTAGGAAATAAGTTTGTTAGGAGTGAATTGTGCCTGGGTAGCCATACTGTTTGTGTTTTGTAAGACCGACTCTCACCTGAGTTAATTGGATAGAGCATTTTAAAGTTTAAAATCAGTAGTGTTATAAAATAACAATAGCTGGCTATCTTTTATATCTGCATGAAATAGGAGAGTTGTTGTTTTCACCATAACAGTTTTAAAATTAGTATTCAATGTGTATCCTCCAAGCTTAGCAAGCCAATTAGTAGCTGGTTAAGTCAGTGCTTAAAAAAAAGAGAGAGAAAACCTATGATCCAGCGGTCCAGGATTCATCTTAACTTTTCCCATTTTTTTACGGAATTTGCAAGCTCGTTTTAAATACTAGCAGAATGCGTTTTGTTTGAAACAAGGTATAGACTAATCCAATGATGTTATTACACATAAGCTTAATATTATGTCGCTTCAGATAACTGATCTGTTGAAATGAGATTTTTGAGAAGCATTTAGTATTATTTGCTCATTTAAAAATGTTCACTGTTTTTCAG
Seq C2 exon
ATGGGGCACCCTGGCATGCATTATGCCCCAATGGGAATGCACCCTATGGGTCAGAGAGCGAATATGCCTCCTGTACCTCATGGAATGATGCCGCAGATGATGCCCCCTATGGGAGGGCCACCAATGGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504:ENST00000410080:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.992 A=NA C2=0.901
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCGGCGCAGAAACTTCCTC
R:
ATAATGCATGCCAGGGTGCC
Band lengths:
343-1572
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