HsaINT0131271 @ hg19
Intron Retention
Gene
ENSG00000204479 | PRAMEF17
Description
PRAME family member 17 [Source:HGNC Symbol;Acc:29485]
Coordinates
chr1:13716088-13717379:+
Coord C1 exon
chr1:13716088-13716404
Coord A exon
chr1:13716405-13716800
Coord C2 exon
chr1:13716801-13717379
Length
396 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TTCCCCTATGTTACTCACAGGAG
3' ss Score
7.55
Exon sequences
Seq C1 exon
TCTAGAGTTTTTCACTGGAGATTTGTCAGAATGAGCCTCCAGTCCCCATCCAGACTCCTGGAGCTGGCAGGCCAGAGCCTGCTGAGGAACCAGTTCTTGACCATCTTCATCCTGGACGAGCTGCCCAGGGAGGTCTTCCCTCTGATGTTCATGGAGGCCTCCAGCATGAGACATTTTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGCCCTTCCTCCGCCTCCCTCTGGGATCCCTGATGAAGACACCTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACTGCTGGCCCAGAAGCTTCGCCCCAG
Seq A exon
GTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTCCAGGCATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGTGGGGTTGGGGAGCTAGGGTGGCTCAGAGGCTTCTGATGGTGCCCATGAGAGACCTTGACCATTGCCCAGATCCTCTGGAAAAGGACTGCTCACCATACAGGGTCCACTGAGGAAACAGGAACCTGCTTCCTCCCAGTGGAAGGTAAAGGTTCTAGAAGTGAGAACCAGGCAGAATCCAAGGGGGAGCGGGATGGAGAAGAGACAGAAGGAGGAGCACTGAGGACAGGAGCAGCTGACTGATGTCCTGGATGTTGAGTGAAAGCTCAGGTCAGGGGTGGGTCTTTGCCTACATTCTGAGCTTTTCCCCTATGTTACTCACAG
Seq C2 exon
GAGGTGGAAACTTCAAGTGCTGGATTTGCGGGATGTTGATGGGAATTTCTGGACTATATGGTCTGGAGCCAGGGCCCTCTCCTGCTCCCCAGAGGCCATGAGTAAGAGGCAGACAGTGGAGGACTATCCAAGGACGGGAGAGCACCAGCCCTTGAAGGTGTTCATAGACCTCTGCCAAAAGGAAAGTACACTGGATGAATGCCTGAGCTACCTCTGCAGGTGGATCCACTACAGAAGAGGTCTAGTGCACCTGTGTTGTAATAAGGTGCAGAATTACTCAATGCCCACTTCAAGTTTCAGAAATTTATTGAAAAGGGTATACCCAGACAGTATCCAGGAGTTGGAAATTAAGAGAAAGTGCTCTCTGAATAAAACAGGAAAGTTTGCCCCTTACTTGAGCCAGATGAGCAATCTTCGCAAACTCTTTTTAGCCTTCGGTTATGACGATGAGTTATATGTAAGCGGCCAACAGCAGTTCGTTCCTGACTTGGACTGTCCATTCCTCTGCCTGTACTACCCTCAGATGCTTTATATAAGAAAGATCAGTAATATCAAAGAGCACCTGGAGCACCTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204479-PRAMEF17:NM_001099851:1
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=0.031
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:
CTCCAGTCCCCATCCAGACTC
R:
GCCCTGGCTCCAGACCATATA
Band lengths:
356-752
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)