DreINT0078195 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34256202-34256573:-
Coord C1 exon
chr20:34256454-34256573
Coord A exon
chr20:34256329-34256453
Coord C2 exon
chr20:34256202-34256328
Length
125 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
TCACTTTTGCCTATGGACAGACA
3' ss Score
5.4
Exon sequences
Seq C1 exon
ATATTAATGAGTGTGAACAGAGGGATACATGTCAGCACGAGTGTATGAACACTCCAGGCAGCCATAGGTGTTTGTGTCCCAGCGGCTATCGGCTTATGACCAACGGAAAAACCTGCCAAG
Seq A exon
GTAAAACAATTAAGATGTACAATAAAAAACTACATCATATATGTGCTAACCTAACCAGAGTGTGACCTGTAACAAACAAAAATAAGGAAAATCATTTTGCATTGCTCACTTTTGCCTATGGACAG
Seq C2 exon
ACATAGATGAATGCCTAGAGCAGAACATTCAGTGTGGTGCAAACAGGATGTGTTTCAACATGAGAGGGAGTTACCAGTGTATCGACACACCTTGCCCACCCAATTATCAGAGAGATCCTGCCACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:105
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:
PF126622=cEGF=PU(83.3=48.8)
A:
NA
C2:
PF126622=cEGF=PD(12.5=7.0),PF129472=EGF_3=WD(100=81.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAATGAGTGTGAACAGAGGGATACA
R:
CTGTGGCAGGATCTCTCTGAT
Band lengths:
242-367
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]