DreINT0077669 @ danRer10
Intron Retention
Gene
ENSDARG00000045544 | hgfa
Description
hepatocyte growth factor a [Source:ZFIN;Acc:ZDB-GENE-041014-2]
Coordinates
chr4:19740224-19740628:-
Coord C1 exon
chr4:19740486-19740628
Coord A exon
chr4:19740345-19740485
Coord C2 exon
chr4:19740224-19740344
Length
141 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
GTTTATGTGTGTGTTCATAGTGG
3' ss Score
6.43
Exon sequences
Seq C1 exon
TTTTAAGCCTACCAGACACAAAAAGTCTGACCTACGTCAGAACTTTTGCCGAAATCCAGACAATGATCCAAATGGGCCCTGGTGCTTCACTGAACTCACTGAGACCCGGCACCAGGATTGTGGACTGCCTCAGTGTTCAGATG
Seq A exon
GTAAGACATCACCTCATCTTGACTTCACTATTTTTTTTTCAGTGCATAGGTGGTATTGGTGAACTTGTCTGCGTAATATCTGTGCATTTGGAGTGTTTAATTCCAAATACACGCATAACATGTTTATGTGTGTGTTCATAG
Seq C2 exon
TGGAGTGTATGAAATGTAATGGGGAAACCTACAGAGGGCCCATGGATCATACAGAGAGTGGGAAAGAGTGCCAGAGATGGGACTCGCAGAAACCTCATAAACACACCTACCAGCCTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000045544:ENSDART00000100952:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.224 A=NA C2=0.366
Domain overlap (PFAM):
C1:
PF0005113=Kringle=PD(57.0=91.8)
A:
NA
C2:
PF0005113=Kringle=PU(48.7=92.7)
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:
AGCCTACCAGACACAAAAAGTCT
R:
TGTGAGGCTGGTAGGTGTGTT
Band lengths:
258-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]