DreINT0087998 @ danRer10
Intron Retention
Gene
ENSDARG00000020785 | lama4
Description
laminin, alpha 4 [Source:ZFIN;Acc:ZDB-GENE-040724-213]
Coordinates
chr20:256938-257300:+
Coord C1 exon
chr20:256938-257080
Coord A exon
chr20:257081-257170
Coord C2 exon
chr20:257171-257300
Length
90 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
GATAATTGGATGTCCAACAGGCC
3' ss Score
5.52
Exon sequences
Seq C1 exon
GTGTCTGTGATCTATCATCATTCAAAGAAGATCATTTTGTTGGTGGACAGAAGCCATGTCAAGTCCTTTGAAAGTGAAAAGAAACCCCTACCCTTTTCTGATATCTATATAGGAGGAGCTCCTTCGAGAATTCTGCAGTCTAG
Seq A exon
GTAAGATCATATGCTCCAAATAAAGCGCAGAGAAATCAACTACCATTACTGATTTCTTACTTTTAACCAAGATAATTGGATGTCCAACAG
Seq C2 exon
GCCAGAGCTGACATCCTTGATTGGATTGAAGGGTTGTGTAAAAGGCTTCCAGTTCCAGAAAAAGGATTTCAACCTCTTGGAGGAGCAAGGAACCATTGGTATCAGCAGCGGCTGTCCTGAGGAATCGTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020785:ENSDART00000002661:27
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:
PF0221019=Laminin_G_2=FE(36.4=100)
A:
NA
C2:
PF0221019=Laminin_G_2=PD(16.3=47.7)
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:
GTTGGTGGACAGAAGCCATGT
R:
TCCTTTTTCTGGAACTGGAAGCC
Band lengths:
171-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]