GgaINT0035387 @ galGal4
Intron Retention
Gene
ENSGALG00000004620 | LAMC1
Description
laminin, gamma 1 (formerly LAMB2) [Source:HGNC Symbol;Acc:HGNC:6492]
Coordinates
chr8:7489358-7489845:+
Coord C1 exon
chr8:7489358-7489603
Coord A exon
chr8:7489604-7489691
Coord C2 exon
chr8:7489692-7489845
Length
88 bp
Sequences
Splice sites
5' ss Seq
GGGGTACGA
5' ss Score
5.37
3' ss Seq
CATTCCTGCCCTTCCTGCAGCTT
3' ss Score
9.99
Exon sequences
Seq C1 exon
GCAAGAGGTGTGAGCTGTGTGATGATGCCTATTTTGGAGACCCACTGGGTGAAAATGGGGCTGTGAGGCCGTGCCGCCTGTGCCAGTGCAACGACAACATTGATCCCAACGCTGTGGGCAACTGCAACCGGCAGACGGGGGAGTGCCTCAAGTGCATCTACAACACAGCCGGCTTCTACTGCGACCGCTGCAAGGACGGCTTCTTTGGGAACCCCCTGGCCACCAACCCTGCTGACAAGTGCCGGG
Seq A exon
GTACGAGCATTTCCTCTCATGTCTGAAGCTGGTTTGGTCCCTGGGAACTGCCTTGGGGTGATGTTTCCCATTCCTGCCCTTCCTGCAG
Seq C2 exon
CTTGTCACTGTAATCCCTACGGCACCGTGAATCAGCAGACGAGCTGCAACCAAGTGACGGGGCAGTGCGAGTGCCTCTCCCACGTCACCGAGAGGGACTGCAGCGCCTGCGAGCCCGGCTTCTTCAACCTGCAGAGCGGCCGAGGCTGTGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004620:ENSGALT00000039414:14
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:
PF0005319=Laminin_EGF=PD(42.1=28.9),PF0005319=Laminin_EGF=WD(100=65.1)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=94.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGGACGGCTTCTTTGGGAAC
R:
GTTGAAGAAGCCGGGCTCG
Band lengths:
183-271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]