HsaINT0131267 @ hg19
Intron Retention
Gene
ENSG00000116726 | PRAMEF12
Description
PRAME family member 12 [Source:HGNC Symbol;Acc:22125]
Coordinates
chr1:12834984-12836261:+
Coord C1 exon
chr1:12834984-12835297
Coord A exon
chr1:12835298-12835685
Coord C2 exon
chr1:12835686-12836261
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
GCGGTGGAAACTTCAAGTGTTGGACTTGCGGAATGTGGATGAGAACTTCTGGGGCATATGGTCTGGAGCTTCTGCACTCTCCCCAGAGGCCCTGAGTAAGAGACGAACAGCAGGGAACTGTCCAAGGCCGGGTGGGCAGCAGCCCTTGATGGTGATCCTAGACCTTTGCTTCAAGAATGGGATGCTGGATGAATGCCTCACCCACTTCTTAGAGTGGGGCAAGCAGAGAAAAGGCTTACTGCACGTGTGTTGCAAGGAGCTGCAGATTTTTGGAATAGCCATCCACAGGATCATAGAGGTCCTGAACACGGTGGAGCTAGACTGTATCCAGGAGGTGGAAGTGTGCTGCCCGTGGGAGCTGTCCATTCTTATAAGGTTCGCCCCTTACCTGGGCCAGATGAGGAATCTCCGCAAACTTGTTCTCTTCAACATCCATGTCTCTGCCTGCATTCCCCTAGACAGGAAGGAGCAGTTTGTCATCCAGTTCACCTCTCAGTTCCTCAAGCTGGACTACTTCCAGAAGCTTTACATGCACTCTGTCTCTTTCCTCGAAGGCCACCTGGACCAGCTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000116726-PRAMEF12:NM_001080830:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
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
Rat
(rn6)
No conservation detected
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]
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)