DreINT0078191 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34261291-34261615:-
Coord C1 exon
chr20:34261502-34261615
Coord A exon
chr20:34261417-34261501
Coord C2 exon
chr20:34261291-34261416
Length
85 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGT
5' ss Score
7.12
3' ss Seq
TGCTGCTTCTTTCTCCTCAGACA
3' ss Score
10.12
Exon sequences
Seq C1 exon
ATGTAAACGAGTGTCAGGAATCGAACCCCTGCCATCAGCACTGTCTAAACACCATTGGCAGCTTCCGCTGTGCTTGTGAGCCGGGGTACCAACTCAGGAATCGGCGCTGTATTG
Seq A exon
GTATGTTATAAACCTGTCTCCAGGCTTTAATTGCACGGTTGCATAGATTTACTGACCACTTTAATTGCTGCTTCTTTCTCCTCAG
Seq C2 exon
ACATAAATGAATGCAAACAGAGAGTGTGTCGCTCAGATCAGCAGTGTAAAAACACACGTGGTGGATACACTTGCATTGACCTCTGCCCTACTGGCATGACTAAAGGAGGCAATGGCACATGCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:101
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:
PF0764510=EGF_CA=WD(100=94.9),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.3),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATCGAACCCCTGCCATCAG
R:
GCAAGTGTATCCACCACGTGT
Band lengths:
171-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]