HsaINT1027893 @ hg38
Intron Retention
Gene
ENSG00000116726 | PRAMEF12
Description
PRAME family member 12 [Source:HGNC Symbol;Acc:HGNC:22125]
Coordinates
chr1:12774841-12776118:+
Coord C1 exon
chr1:12774841-12775154
Coord A exon
chr1:12775155-12775542
Coord C2 exon
chr1:12775543-12776118
Length
388 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTCTTCTCTTTTACCCACAGGCG
3' ss Score
12.22
Exon sequences
Seq C1 exon
GATGTTTTTTTCTCTAGATTCATCAGGATGAGCCTCCAGGCCCCACCTAGACTCCTGGAGCTGGCTGAGCAGAGTCTGCTGAGAGACCGGGCCTTGGCCATCCCCACCCTGGAGGAGCTGCCCAGGGAGCTCTTTCCCCCACTGTTCATGGAGGCCTTTACCAGGAGATGCTGCGAGACCCTGACAACTATGGTGCAGGCCTGGCCCTTCACCTGCCTTCCTCTAGGGTCCCTGATGAAGTCATGTAATCTAGAGATCTTTCGAGCTGTGCTGGAGGGGCTTGATGCACTGCTTGCCCAGAAGGTTCGCCCCAG
Seq A exon
GTGAGGTGACCCAGCTAACCAGGTGGGGAGGGCTCAGGCATCCAGGGTAGGGTTAGCTGGGTCAGAAGGAGTGGGAGGCCCAAGGGTGGCCCAGAGACTTCTGATGGGGCTGGGGAGGAAGCTCAGAGAGGCCTTGGCCATTGTCCAGCTCCTCTGGGAAAGGACTGCTCACCATGCAGGGTCCACTGAAGGATCAGGAACCTGCCTCCTGCCAGTGGCAATTGAAGACACTAGCAGTGGGGACCAGGCAGGTTTCAAGGAGAAAGAGGGATGGAGAAAAGACAGAGAGTGGGAGAAGCAGCAGGGAGGAGAGTCGCTGATGTCCGGGATGTGGATAAAAGCTCAAATCCTTCCTAAATTTGGAGCCTCTCTTCTCTTTTACCCACAG
Seq C2 exon
GCGGTGGAAACTTCAAGTGTTGGACTTGCGGAATGTGGATGAGAACTTCTGGGGCATATGGTCTGGAGCTTCTGCACTCTCCCCAGAGGCCCTGAGTAAGAGACGAACAGCAGGGAACTGTCCAAGGCCGGGTGGGCAGCAGCCCTTGATGGTGATCCTAGACCTTTGCTTCAAGAATGGGACGCTGGATGAATGCCTCACCCACTTCTTAGAGTGGGGCAAGCAGAGAAAAGGCTTACTGCACGTGTGTTGCAAGGAGCTGCAGATTTTTGGAATAGCCATCCACAGGATCATAGAGGTCCTGAACACGGTGGAGCTAGACTGTATCCAGGAGGTGGAAGTGTGCTGCCCGTGGGAGCTGTCCATTCTTATAAGGTTCGCCCCTTACCTGGGCCAGATGAGGAATCTCCGCAAACTTGTTCTCTTCAACATCCATGTCTCTGCCTGCATTCCCCTAGACAGGAAGGAGCAGTTTGTCATCCAGTTCACCTCTCAGTTCCTCAAGCTGGACTACTTCCAGAAGCTTTACATGCACTCTGTCTCTTTCCTCGAAGGCCACCTGGACCAGCTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000116726:ENST00000357726:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.010
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATCAGGATGAGCCTCCAGG
R:
TGCCCCAGAAGTTCTCATCCA
Band lengths:
351-739
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains