DreINT0077666 @ danRer10
Intron Retention
Gene
ENSDARG00000045544 | hgfa
Description
hepatocyte growth factor a [Source:ZFIN;Acc:ZDB-GENE-041014-2]
Coordinates
chr4:19746897-19747391:-
Coord C1 exon
chr4:19747247-19747391
Coord A exon
chr4:19747010-19747246
Coord C2 exon
chr4:19746897-19747009
Length
237 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACA
5' ss Score
5.49
3' ss Seq
CTATCTTTGCTTCCTTACAGGGC
3' ss Score
11.69
Exon sequences
Seq C1 exon
ATTGCAGAAAACAGACATTGCAGAGGTATCAGAAAAGTGAAAACAGCCGACTGCTTTGTACAGACTGTCCAGAATCCCCTCGAATTAGGAACCTGTCGCTGGAGGAATGCGCACGCAAATGTAGCAAGAGCAAGAAGTCCTGCAG
Seq A exon
GTGACACACACATGATCACTCATACACATTTAAAGTCACAAAAATGTTGACTGTACAATTAAAATCATTGTGGATCAGTGTTGTTTTGGATGGTTGAAGATTAAGGTGACTAAATGTGGATGTAATTGATATTTTTGGATTAACTATTGATTTAACAAGCTTCATCTAAACCTCCTGGATGTCTGACCCAACGATTGTCTTTCGTTTTCTTGGTTTTCTATCTTTGCTTCCTTACAG
Seq C2 exon
GGCATTCTACTTTGACCACATAAACAGGAAATGTCACTTTCTTCCTTTTGACCGTTTCTCCGAAGGCGCGAAGAGAGAGCGAAAACCCAGTTGTGACCTTTACGAGAAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000045544:ENSDART00000100952:2
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:
PF0002421=PAN_1=PU(54.0=95.9)
A:
NA
C2:
PF0002421=PAN_1=FE(43.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGCAGAAAACAGACATTGCAGA
R:
TTCTCGTAAAGGTCACAACTGGG
Band lengths:
252-489
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]