DreINT0078199 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34331667-34332125:-
Coord C1 exon
chr20:34331998-34332125
Coord A exon
chr20:34331781-34331997
Coord C2 exon
chr20:34331667-34331780
Length
217 bp
Sequences
Splice sites
5' ss Seq
TTGGTCAGT
5' ss Score
5.07
3' ss Seq
ATCTTTGAACCCCTCTGTAGAGT
3' ss Score
6.38
Exon sequences
Seq C1 exon
GCACAGAATGACTCCTGATGGCACACTGATCATCAAGAACACAGGGCTGAAGGATGCTGGGACATACGGCTGCTTGGCGAGTAATGTGGCAGGAACAGACTCTCAAACTGCCATAGTCAGCTACATTG
Seq A exon
GTCAGTAAACAAAAACAACAACAAAAAAATACTAATAATATATATATATATATATATATATATATATATATATATATATATATATATATATTTTTTTTTTTTACCTCTAAACTTCTCACAACTGTAAATAAGTTAGACATTTGACATACTCAGTCCCACCCTGTAGTTATACTCTAGTCTTAATTAAGTTTCCTGTGATCTTTGAACCCCTCTGTAG
Seq C2 exon
AGTCTCCACAGGTGACGGTCCCTCACTCTGACCTGCTGATTGGTCTGGGACAGAAAACTGTAATGGAGTGCAGGGTCACAGGAGTCCCACATCCTGACATCATGTGGTACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:13
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(46.5=90.9)
A:
NA
C2:
PF0767911=I-set=PU(40.9=92.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACAGAATGACTCCTGATGGC
R:
ACCACATGATGTCAGGATGTG
Band lengths:
236-453
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]