DreINT0017183 @ danRer10
Intron Retention
Gene
ENSDARG00000036493 | PRAMEF1
Description
PRAME family member 1 [Source:HGNC Symbol;Acc:HGNC:28840]
Coordinates
chr7:39822780-39823347:+
Coord C1 exon
chr7:39822780-39822984
Coord A exon
chr7:39822985-39823063
Coord C2 exon
chr7:39823064-39823347
Length
79 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
TAATCCTCGTTTGTGCGCAGATG
3' ss Score
7.68
Exon sequences
Seq C1 exon
AAAACATCCATTACTCAACAACTTCGCTCTTATTAAATCCTATATTTAGGTTTATCAGACGTTTAAGACGCTCGCGACATTGCGATGGCGGTTAAACAAGACTAATAGAAAGGAGCATGTAGTTCGTTTGCAGGATGACAGTGATGAGGGAGGTCGTTTTTAGGCTGCTTTAGAGACACCCTGGCGCTTTAGTGGATAAATGAAG
Seq A exon
GTATGACCTTCTCTTTCTTCCTCTCTCGTGTCTGTCATTTGGTTTGTGTGTCAAAGTAGTAATCCTCGTTTGTGCGCAG
Seq C2 exon
ATGGTTCTGTCTTTGGTGAATCTGTGCGCCCGGGAGGTGGTGAGCGATCATAGCTCTTCGCCCTACTGGCTGAGCTGTGTGCCCAGAGAGCTTTACCAAGCCCTGCTTGACGCTGCCTTCACCCACTGCCGTCCTCTCGCCGTGGGCGAGCTCGTCCAGCGGTGGCCCGAGCGAACGCTTACCACTGGAGGCAGCAGAAGAGTGGGAAAGTCTCAGTGTCCTCCGAACCGCCTCTGCGTCCAGGCTCTGCTGCTGGCCGTGGTCAGAGGACTCTCGGACAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036493:ENSDART00000053011:1
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=0.042
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCGATGGCGGTTAAACAAGA
R:
AGCTATGATCGCTCACCACCT
Band lengths:
180-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]