DreINT0078226 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34302645-34303057:-
Coord C1 exon
chr20:34302881-34303057
Coord A exon
chr20:34302797-34302880
Coord C2 exon
chr20:34302645-34302796
Length
84 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
GATGTATTCTGTTGTTTTAGTTC
3' ss Score
7.31
Exon sequences
Seq C1 exon
CTGTGACGTGGTATAAAGATGGACGCCCATTAACAAGTGCTGCAGGGGTTAATATTCTGAGCAGAGGTCATGTACTGGAGATCGACCGTGCGCAGGTGTCAGATGCAGGATTCTACAAGTGTGTGGCCATCAATGTGGCCGGCAGCACTGAGCTCACATACAGTCTACAGGTGTATG
Seq A exon
GTGAGTGTGTGTGTCTCTCACCAAAACAATTCAGTTGTAACTTCTCTCTTGGTTTTAATCATCTGATGTATTCTGTTGTTTTAG
Seq C2 exon
TTCCTCCCACTATCTCCAGTAAAGGAGGAATGGTAACAGTGGTGGTGAATGATCCAGTCAGGTTAGAGTGTGAAGCCTCTGGAGTTCCTGTGCCCAGCCTCACCTGGCTAAAAGAGGGCAGTCCTGTCTCCAGCTTCTCAGATGGCATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(67.9=95.0)
A:
NA
C2:
PF0767911=I-set=PU(53.9=94.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGTGTGGCCATCAATGTGG
R:
CTGCCCTCTTTTAGCCAGGTG
Band lengths:
181-265
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]