DreINT0073860 @ danRer10
Intron Retention
Gene
ENSDARG00000036295 | golga7ba
Description
golgin A7 family, member Ba [Source:ZFIN;Acc:ZDB-GENE-050417-14]
Coordinates
chr1:54249404-54249852:+
Coord C1 exon
chr1:54249404-54249556
Coord A exon
chr1:54249557-54249750
Coord C2 exon
chr1:54249751-54249852
Length
194 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
GTGTGTGTGTGTGTGTGCAGGTG
3' ss Score
10.65
Exon sequences
Seq C1 exon
ATCGAGCGGACGCTGTTTGAGGACACGGTGAAGACGCTGAATACTTACTATGCAGAGGCGGAGAAGATCGGAGGCCAGTCTTACATAGAAGGATGTCTGGCCTGCCTTACAGTTTACCTCATCTTCCTGTGCATCGAGACGCGTTACGAGAAG
Seq A exon
GTAAGCTATCAGCATATTAAACATAGTAAACACAGACGAATTGGTGTTGTTTGCAAATGTGTGTTGATTTTTGCAGAATATGGGGAATGAAAATTATGCTGATTGTCAAAAGCGTGTGTGTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCAG
Seq C2 exon
GTGCTGAAGAAGATCTCGCGCTACATTCAGGAGCAGAATGAGAAAGTTTACGCTCCTCGAGGTCTCCTCATCACAGACCCGATAGAGAGAGGCATGAGGGTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036295:ENSDART00000089603:3
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:
PF054786=Prominin=PD(51.7=90.2),PF102564=Erf4=FE(43.5=100)
A:
NA
C2:
PF102564=Erf4=FE(28.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGTTTGAGGACACGGTGAA
R:
ACCCTCATGCCTCTCTCTATCG
Band lengths:
243-437
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]