DreINT0077667 @ danRer10
Intron Retention
Gene
ENSDARG00000045544 | hgfa
Description
hepatocyte growth factor a [Source:ZFIN;Acc:ZDB-GENE-041014-2]
Coordinates
chr4:19746374-19747009:-
Coord C1 exon
chr4:19746897-19747009
Coord A exon
chr4:19746489-19746896
Coord C2 exon
chr4:19746374-19746488
Length
408 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
GTGCTGTATGTTCTCCACAGACT
3' ss Score
9.65
Exon sequences
Seq C1 exon
GGCATTCTACTTTGACCACATAAACAGGAAATGTCACTTTCTTCCTTTTGACCGTTTCTCCGAAGGCGCGAAGAGAGAGCGAAAACCCAGTTGTGACCTTTACGAGAAGAAAG
Seq A exon
GTAAATATTTTTTATTCCCTTTCGAAGAAGTTCGCTCACACTTGATTTTTTTTAGCTTCCTGGAAATTCCTGTACAACTGTGCCAGTTGTGTTTGTTTAGATCCCTGGCTTTACGTGTAAAATCGTATAAAGTCATCTTCGTCATCGTAAACAGCACATGCTGAAGTCATTTGGCAGCAGACAGAGCATGAGAAACCATGAGCGATAAGTGTTGACGCTTACAAGATGGCGTATGTTTATGCTTCCAGTAAGAGTCGGAGCTGAAATGTAGATTTATGCCGTAATCATCAGTAACACTCTTGTTTGGAGGCTTAAATCACCTCAGGACGTCAGCAAAATGTGTAATCTCTAAACAAAATTCATCGTTATGGATTATATGAATGTTTGTGTGCTGTATGTTCTCCACAG
Seq C2 exon
ACTATGTGAGGGAGTGCATCATTGGGTCAGGTGTCAACTACAAGGGGAGAAGGTCATTCACAAAGACTGGAATTACGTGCCAATCCTGGAATATGTCCGTCCCACATGAGCACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000045544:ENSDART00000100952:3
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=0.051
Domain overlap (PFAM):
C1:
PF0002421=PAN_1=FE(43.7=100)
A:
NA
C2:
PF0002421=PAN_1=PD(1.1=2.6),PF0005113=Kringle=PU(41.8=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCATTCTACTTTGACCACATAAACA
R:
TGCTCATGTGGGACGGACATA
Band lengths:
225-633
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]