DreINT0078289 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34265808-34266146:-
Coord C1 exon
chr20:34266009-34266146
Coord A exon
chr20:34265930-34266008
Coord C2 exon
chr20:34265808-34265929
Length
79 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TACACTTGCATTGATCTTAGGAG
3' ss Score
5.52
Exon sequences
Seq C1 exon
GGCCTGCTATGAGGAAGCTGATATCCATCCTGAACCCAATATACTGGACCACAGCACATGAGCTGGGTGAAGCTGTCAATGGCTTCACCCTCACTGACGGCATTTTCAGACGTGAGACTCAGGTGGAGTTTGCCACAG
Seq A exon
GTAAGAGAAATCACCTTGATGTTTAGAGAATCTTCAAATGATGTTTTCCTCATTGAAATTACACTTGCATTGATCTTAG
Seq C2 exon
GAGAGATTTTGAGAATGACCCATGTGGCACGAGGGCTGGACTCAGATGGAGCACTTCTACTGGACATTGTAGTAAATGGACACATTCTGCAGCTGCCGTCCAACGCTGACATCAGTCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:95
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:
PF074747=G2F=FE(24.6=100)
A:
NA
C2:
PF074747=G2F=FE(21.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCTGCTATGAGGAAGCTGA
R:
GTGCCACATGGGTCATTCTCA
Band lengths:
168-247
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]