DreINT0088007 @ danRer10
Intron Retention
Gene
ENSDARG00000020785 | lama4
Description
laminin, alpha 4 [Source:ZFIN;Acc:ZDB-GENE-040724-213]
Coordinates
chr20:265394-266024:+
Coord C1 exon
chr20:265394-265549
Coord A exon
chr20:265550-265864
Coord C2 exon
chr20:265865-266024
Length
315 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTG
5' ss Score
8.35
3' ss Seq
TCTTTCTTCTCCTACTTTAGAGG
3' ss Score
8.52
Exon sequences
Seq C1 exon
ATTATCTTTATCAGAGCTGGAAATATGGGCAGAATGCTAATCGATGGTCTTACGGTATTAGAGGACAGAGCTCCAGGCAGAAACACCTCGCTGCTTGTCCAGGACCCTCTCTATGTTGGCGGAGTCCCACCTCATCAGGCCATGAAAAACATTCAG
Seq A exon
GTATTGTGCTCTCAGGTTATTCATTCATTCAGCTTTCTTCAGTCCCGTACTTATCAGAGGTTGCCACAGTGGAATGAACCACCAACTATTTTATGTGTTTTACATGGCGGGTGCCCGTCCAGCAGCAACCCAGTACTGGAAACATTAGTATTGTATTCTATGTCTCTCCATTTATGTGTTTGGTAAATATCATTCATAAATCTGCTTGTGTTCTGTTGTGATCAGCCCTCTCAAGTATATTTCGAGATGTTGTTGAGGAGGAAAGGGTGTAATGGAAAGTGTGAGGTTCAACAACTCTTTCTTCTCCTACTTTAG
Seq C2 exon
AGGACATCTGTGTCGAGTTTCACTGGCTGTGTGCGGAGTCTCCAGCTGAATGGCCGCTCGCTCACCTCTGCCTCCCACAGTTTTGGGGTCACCCCCTGCTACGAGGGCCCCTCGGAACCGGGGACGTACTTCGCTGAGGAGGGAGGATATGTGCTGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020785:ENSDART00000002661:35
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=0.019
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=FE(39.8=100)
A:
NA
C2:
PF0221019=Laminin_G_2=PD(14.1=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTATCAGAGCTGGAAATATGGGCA
R:
CCAGCAGCACATATCCTCCCT
Band lengths:
310-625
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]