GgaINT0020357 @ galGal3
Intron Retention
Gene
ENSGALG00000006937 | P4HTM
Description
NA
Coordinates
chr12:11929179-11929606:-
Coord C1 exon
chr12:11929421-11929606
Coord A exon
chr12:11929270-11929420
Coord C2 exon
chr12:11929179-11929269
Length
151 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGG
5' ss Score
10.48
3' ss Seq
CTGCTCTGTCCTGTCTGCAGGTA
3' ss Score
11.7
Exon sequences
Seq C1 exon
GGTAATGCGCCTGACTCGCCTGCCCCCAGAGATTGTGGAGCACAGTGAGCCCCTGCAGGTGGTGCGCTATGACCAGGGGGGCCACTACCATGCCCACATGGACAGCGGCCCCGTCTTCCCCGAGACCGCCTGCAGCCACACCAAGCTGGTTGCCAACGAAAGCGCTCCCTTCGAGACCTCATGTCG
Seq A exon
GTAAGGGCCGCTTTGGTGCAGCTCTCTGTTGCCTTTGGAAAAAAAATGACGTCAACTGCATGTCTCGTGCTGTCTTGGAGGAGTGGTGTACATACAGCAGCTCCTCCTGCTCCAGCTGTGTCCCCTGACAGCTGCTCTGTCCTGTCTGCAG
Seq C2 exon
GTATGTGACAGTGCTGTTCTACCTGAACAATGTGACGGGTGGCGGAGAAACTGTCTTTCCTATAGCTGATAACAGGACGTATGAAGAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006937:ENSGALT00000011237:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF136401=2OG-FeII_Oxy_3=PU(30.1=69.8)
A:
NA
C2:
PF136401=2OG-FeII_Oxy_3=FE(20.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCAGAGATTGTGGAGCACAG
R:
TCTTCATACGTCCTGTTATCAGCT
Band lengths:
249-400
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]