DreINT0088238 @ danRer10
Intron Retention
Gene
ENSDARG00000036279 | lamc1
Description
laminin, gamma 1 [Source:ZFIN;Acc:ZDB-GENE-021226-3]
Coordinates
chr2:35981211-35981608:+
Coord C1 exon
chr2:35981211-35981333
Coord A exon
chr2:35981334-35981418
Coord C2 exon
chr2:35981419-35981608
Length
85 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
GGAACGTTTGATTTCTGTAGATA
3' ss Score
4.79
Exon sequences
Seq C1 exon
ATGATGAAGGCTGGAAGGGTAAACAGAGAGATGACTCCAGTGTACCGGTACAGTGGTCACCCAGTTCTGGAGAGATCTCACTCATCTCAGAAGATTACTTCCCCATCTACTTTGTGGCTCCAG
Seq A exon
GTACAGTAACAGATGTGGTGTTATAAGCAGGCAGAGGATACGGTGCCTTGTTGGTGTAATCATCTGGAACGTTTGATTTCTGTAG
Seq C2 exon
ATAAATTTCTGCATAATCAGCTGTTGAGTTATGGTCAGAACCTCACGCTGAACTTCAGGATTCAGCGTCACGATGCTCGCCTCTCAGCAGAGGACGTTGTGCTGGAGGGCTCGGGGCTTCGTGTCGCTGTGCCTCTTATTGCTCAGGGTAATTCCTACCCAGGAGAGGAGACCCAAACCTTTGTGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036279:ENSDART00000004277:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.381 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005213=Laminin_B=PU(3.8=11.9)
A:
NA
C2:
PF0005213=Laminin_B=FE(48.1=100)
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:
TGGTCACCCAGTTCTGGAGAG
R:
CACAACGTCCTCTGCTGAGAG
Band lengths:
171-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]