GgaINT0035383 @ galGal4
Intron Retention
Gene
ENSGALG00000004620 | LAMC1
Description
laminin, gamma 1 (formerly LAMB2) [Source:HGNC Symbol;Acc:HGNC:6492]
Coordinates
chr8:7486252-7486833:+
Coord C1 exon
chr8:7486252-7486441
Coord A exon
chr8:7486442-7486720
Coord C2 exon
chr8:7486721-7486833
Length
279 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
AGCATGGCTCTTCTCCCTAGGCT
3' ss Score
7.98
Exon sequences
Seq C1 exon
GCAAATTCTTGGGCAACCAAGTTTTGAGCTACGGTCAGAACCTGACCTTCTCCTTCCGTGTGGACAGACGGGACACACGTCTCTCAGCAGAGGACCTGGTACTGGAAGGGGCCGGGCTGCGTGTGTCGGTGCCTCTCATTGCCCAGGGCAACTCGTACCCCAGTGAGAGCCCACTGACCTACACCTTCAG
Seq A exon
GTGAGGGGGTCCAGCCCAGCCCAATGGGAGCCCAGAGAGCAGGTGGGACCCAGTCTGCCACACACCCTGCCCTCTCAGCTCCTGGGAAAAGAAACAGCAGTAATTTTAGCTCATGAGAGTGGTCTTATCAGGTTAATTTGAAGCTGGCTGTTCAGCAGGTTGCTTAAGTGGATGCAGAGTATGTGGCAATTGCATACCTTGGTTGGAAATGGTGCTTTAAAAGGGCACAGCTGCTAGCATCTGAAAGCTTTGCAAATGGAGCATGGCTCTTCTCCCTAG
Seq C2 exon
GCTCCATGAGGCTGCTGATTACCCGTGGAGGCCTGCTCTCTCTGCATTTGACTTCCAGAAGCTTCTCCACAATTTGACTGCCATCAAGATCCGTGGAACATACAGCGAGAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004620:ENSGALT00000039414:10
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:
PF0005213=Laminin_B=FE(48.1=100)
A:
NA
C2:
PF0005213=Laminin_B=FE(29.0=100)
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:
GGCAACCAAGTTTTGAGCTACG
R:
TTCTCTCGCTGTATGTTCCACG
Band lengths:
292-571
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]