DreINT0078301 @ danRer10
Intron Retention
Gene
ENSDARG00000079327 | hmcn2
Description
hemicentin 2 [Source:ZFIN;Acc:ZDB-GENE-030131-9765]
Coordinates
chr8:32748096-32748453:+
Coord C1 exon
chr8:32748096-32748239
Coord A exon
chr8:32748240-32748331
Coord C2 exon
chr8:32748332-32748453
Length
92 bp
Sequences
Splice sites
5' ss Seq
ACAGTGCTA
5' ss Score
-10.69
3' ss Seq
GTTGTGTCTTGAAATGACAGGAG
3' ss Score
2.48
Exon sequences
Seq C1 exon
GTCCTTTGTTGCGAGTGCTTGTGTCTGTATTTGCCCCGGTATACTGGACAACAGTGTATCAAACACAGGAAACCCAGAATGGCTTCTCCATCACTGAAGGGCAGTTCAGACAGGAATCTCAGCTAGAGTTTGAAACAGGTTACA
Seq A exon
GTGCTAATGCTCTAATAAGACATGTAGCTGTAAATGAGGACGAGACCATTACATTGTGGATCCTGAATGTGTGTTGTGTCTTGAAATGACAG
Seq C2 exon
GAGAGATTTTAAAGCTGACACACGTGGCAAGAGGTCTGGATGGAGAGGGAGTTCTGTTGGTAGATATTGTTATCAATGGATTTGTTCCTCCTATGCTTTTGTCCTCTAATCTCAATCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079327:ENSDART00000137897:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF074747=G2F=FE(24.7=100)
A:
NA
C2:
PF074747=G2F=FE(21.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGTTGCGAGTGCTTGTGTCT
R:
TGCCACGTGTGTCAGCTTTAA
Band lengths:
168-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]