DreINT0078262 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34279508-34279816:-
Coord C1 exon
chr20:34279735-34279816
Coord A exon
chr20:34279645-34279734
Coord C2 exon
chr20:34279508-34279644
Length
90 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
ATGGTAATCTGCTCCAACAGTTC
3' ss Score
4.88
Exon sequences
Seq C1 exon
GTGGAGAACACTGGCAGATACACCTGTTTAGCCTCTAGCCCTGCTGGAGATGATGATAAAGAGTTTCTTGTTAGAGTACATG
Seq A exon
GTGAGTTTTTAAAGCAATTACAATGTGATAATCAAATTAAAATGTGGCCTTTCCTACAGTAATAGACAAAATGGTAATCTGCTCCAACAG
Seq C2 exon
TTCCACCCAATATTGCTGGAGACAGAGGTGTGCAAGATGTGTCTGTCCTGCAGAACAGACAGGTCACCCTGGAATGTAAATCAGATGCAGTTCCACCTCCAACCCTCACCTGGCTTAAAGACGATGCACCTCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:70
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.214 A=NA C2=0.109
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(29.1=89.3)
A:
NA
C2:
PF0767911=I-set=PU(45.3=84.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCCTGCTGGAGATGATGAT
R:
CGTCTTTAAGCCAGGTGAGGG
Band lengths:
169-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]