DreINT0109510 @ danRer10
Intron Retention
Gene
ENSDARG00000075209 | p4htm
Description
prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) [Source:ZFIN;Acc:ZDB-GENE-110131-7]
Coordinates
chr6:40740554-40740878:-
Coord C1 exon
chr6:40740788-40740878
Coord A exon
chr6:40740678-40740787
Coord C2 exon
chr6:40740554-40740677
Length
110 bp
Sequences
Splice sites
5' ss Seq
GCGGTGTGT
5' ss Score
5.95
3' ss Seq
TGTGTGTGTGTATTTCCCAGTCT
3' ss Score
8.16
Exon sequences
Seq C1 exon
GTACATCACAGTTCTGTTTTACCTTAATAATGTTCAGGAAGGAGGCGAGACCACCTTTCCAGTTGCAGACAACAGAACTTATGAAGAAGCG
Seq A exon
GTGTGTTTTGTTCATAAAATGTTTTTGCATATATGTCAAATACATGAGTTGTGTTCAATTTAAGCACATAATGAGAGGCGTGTGTGTGTGTGTGTGTGTGTATTTCCCAG
Seq C2 exon
TCTCTAATACAGAATGATGTGGATCTATTGGACACCAGGAAACATTGTGATAAAGGCAACCTGAGAGTGAAGCCTGTAAAGGGGACGGCGGTTTTCTGGTACAACTATCTCTCCGATGGTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075209:ENSDART00000154916:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.161 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF136401=2OG-FeII_Oxy_3=FE(20.5=100)
A:
NA
C2:
PF136401=2OG-FeII_Oxy_3=FE(28.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTACATCACAGTTCTGTTTTACCTT
R:
ACCATCGGAGAGATAGTTGTACCA
Band lengths:
211-321
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]