DreINT0109507 @ danRer10
Intron Retention
Gene
ENSDARG00000075209 | p4htm
Description
prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) [Source:ZFIN;Acc:ZDB-GENE-110131-7]
Coordinates
chr6:40743003-40743361:-
Coord C1 exon
chr6:40743265-40743361
Coord A exon
chr6:40743166-40743264
Coord C2 exon
chr6:40743003-40743165
Length
99 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAAG
5' ss Score
5.39
3' ss Seq
CTTTATGCATGCCTCTCCAGGTC
3' ss Score
9.25
Exon sequences
Seq C1 exon
ATATTGACACATTCTCGAGTAAGAGATGGAATCTGGTTAACTTCTGAGAATCTTAAGGAAATTTATGACGGCCTGAAAGCTGATCTGGATGGAAATG
Seq A exon
GTAAAGACCCAAGCTGGAGATATTATTTAAACTTCACATCATAACTTTAGAAGATATAAGAGTGTCCAGATTCATACCTCTTTATGCATGCCTCTCCAG
Seq C2 exon
GTCTCCTGAGTTTAGAGGAGTTTGGGCGTCTGAGAAGTGATGCTTTTCAGCGTTTTCTGCTTCAGCGCGGGGTGGAGAGGAGTCAGCTGGTGAGAAACAGCAGACATACTTGGCTCTATCAGGGTCAGGGAGCACATCAGGTTCTTCAAGACCTCCGCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075209:ENSDART00000154916:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=FE(51.6=100)
A:
NA
C2:
PF134991=EF-hand_7=PD(16.1=18.2)
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:
ATGACGGCCTGAAAGCTGATC
R:
TGTGCTCCCTGACCCTGATAG
Band lengths:
169-268
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]