DreINT0078218 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34309713-34310242:-
Coord C1 exon
chr20:34310088-34310242
Coord A exon
chr20:34309992-34310087
Coord C2 exon
chr20:34309713-34309991
Length
96 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATT
5' ss Score
5.73
3' ss Seq
TTTCATTCGGCATCCCTAAGTGC
3' ss Score
1.33
Exon sequences
Seq C1 exon
GCCAGTGTTTCTGGGTGACCCCAACATTGAAGTTTTAAACAGAGGACAGCAGTTGAAGATAAAGAGCGCTCGCTTGGGGGACCAGGCACGATACCAGTGCAGCGCTACCAACGCAGCAGGAAAGCAGTCCAAAGATTTTAACCTCAGTATATTTG
Seq A exon
GTAATTTTGCTCTTATTATTGATTTTGCATCAACAGAATAGAAAAAAATTCTAAATGCTAAATGTCCTGTCTGTCTTTTCATTCGGCATCCCTAAG
Seq C2 exon
TGCCACCCAGTATTAAAGGAGGAAACGTGTCTTCTGAGGTGACCGTTCTGCTGGGTAACCTGGTGACTCTGGAGTGTGAGGTGCGTGGTGTGCCACTGCCTGCCGTCACATGGTACAAAAATGGAGAGGTCATTCTGTCTAGCAGACAGGCCCAGTATGTGGACCGAGGGCAGTTCCTCAAGATCTTAAGAGCTCAAGTTTCTGATGCTGGACAGTACACATGTAGAGTCACCAGTGTGGCTGGCACTGCTGAAAAAGTTGTCGAGTTGGATGTGTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:30
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:
PF0767911=I-set=PD(57.5=94.3)
A:
NA
C2:
PF0767911=I-set=WD(100=91.5)
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:
CTACCAACGCAGCAGGAAAGC
R:
TTTGTACCATGTGACGGCAGG
Band lengths:
170-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]