DreINT0078267 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34277159-34277606:-
Coord C1 exon
chr20:34277450-34277606
Coord A exon
chr20:34277281-34277449
Coord C2 exon
chr20:34277159-34277280
Length
169 bp
Sequences
Splice sites
5' ss Seq
CAGGTTCAG
5' ss Score
2.78
3' ss Seq
AGTTTGCAATCTGTCCTCAGGCT
3' ss Score
7.16
Exon sequences
Seq C1 exon
TGCCCCCATCCATTGCTGAGGGTCCTACTAACATCACTGTGACAGTGAATGTCCAGACAACACTATCCTGTGAGGCCACTGGTATCCCCAAACCCTCTGTCAGCTGGACCAAAAACACTCAAGCCCTTAACACTGACCAAAACCAGAATATGTACAG
Seq A exon
GTTCAGCCAGGTTTCCTCCCTCTCTTTATATCACCTCTTACTGTACCTTTAAACCAATTGAGCATTACTCTTAAATTTGGGTCTGAAATGACCATAAAGCTAGATATTGCTCCATATCACATTCAATTCATGACTGTATACAGTTTATCAGTTTGCAATCTGTCCTCAG
Seq C2 exon
GCTTTTGTCGTCAGGCTCTCTGGTGGTCATCGCACCGTCAGTAGAGGACACGGCGCTGTACGAGTGTGTTGTGTCCAATGAGGCAGGCCAGGAGAGCAGAGCCATTCAGCTGACTGTACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:75
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.189 A=NA C2=0.024
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(55.6=94.3)
A:
NA
C2:
PF0767911=I-set=PD(43.3=92.9)
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:
TCCATTGCTGAGGGTCCTACT
R:
CTGAATGGCTCTGCTCTCCTG
Band lengths:
258-427
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]