GgaINT0035381 @ galGal4
Intron Retention
Gene
ENSGALG00000004620 | LAMC1
Description
laminin, gamma 1 (formerly LAMB2) [Source:HGNC Symbol;Acc:HGNC:6492]
Coordinates
chr8:7485093-7486161:+
Coord C1 exon
chr8:7485093-7485229
Coord A exon
chr8:7485230-7486038
Coord C2 exon
chr8:7486039-7486161
Length
809 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAAA
5' ss Score
3.23
3' ss Seq
GTTGCACATTTGGCTTTCAGGAG
3' ss Score
6.21
Exon sequences
Seq C1 exon
ATGCAAACCTGGGTTTTTCCATCTGGATCCCTCAAATCCAAGAGGCTGTACCCCCTGCTTCTGTTTTGGACACTCTTCGGTTTGCACCAATGCCATTGGCTACAGCGTGTACAGCATCACCTCCAGCTTTCAGTTTG
Seq A exon
GTAAAATGAGCCTTTCTTTGTATCTCAGGTTGGATTGTAGATGAAAGTGGGACAAGCCCTGCTCCCTCTTCCCTGTGTGAGATTGCAAACTTTGGGTGCAATCCCTAATTCCCTTTTTTGGGAAGCACGGAGCTACTGAAGTCAATGAGAGCTTCCCCATCTTCAGGTTGTTTGTTCTGTTGGGGGGGGGGGAAGAATTCATGGCTTTGCCCTCAGGCACCGAGTGCATGCAGTTGTAAGTGGGCACTGCACATGTAAAACTTCATACCTCAGAAGAGAGGTGCTAGAGAAGGAGGGGTATTTTCTCCATTTTAGAACTGAATCAGGAGTTTGATGGAGAGGGATTATAACTGCTTCAGGTTTTGGGTTGCTTGGCTCTGAATGAAATGTGGTTGTGTTTCTGATGGGCCCGTGAGCTGGGCAGAAATCTTTTTTCATACAGTCTGTTTCCTGCTTTCCTGCATATGAATGTTTTCATTCTGCATAGTCTAAAAAGAACATTTCTAATTAAAATTCCAATGGAGAACGGTTCTTACAAAGGCTGAAACTTGCATAAAGTCATTGCTGACTGCAGGTTTCCCAGTCTTTTCCTGAGGTCTTCAGAAATCAAGATGTTAAACAAGTATTTTTTTTTGTAATGTTCAGAGTTCAGAAGGCTCAAGTCAGCAGTCTGGATATGCTGTGTATGTCCTGCACAGTACCAGCATATGGAATAGGGATGGGTTATATATGAGCAGTTTGCAATATGACATAATGTGTGTAGAGCTGCTCCTTTGAATGATGTTGAGTGTTGCACATTTGGCTTTCAG
Seq C2 exon
GAGAGGACGAGTGGCACGCTGAGCAACGTGACGGCTCCCAGGTCCCTCTGCAGTGGAGTTCAGAGACCCAGGACATCTCTGTCATCTCAGACAGCTACTTCCCCATCTATTTTGTTGCACCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004620:ENSGALT00000039414:8
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=0.119
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(33.3=34.0)
A:
NA
C2:
PF0005213=Laminin_B=PU(3.8=11.9)
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:
ACCTGGGTTTTTCCATCTGGA
R:
GTGGTGCAACAAAATAGATGGGG
Band lengths:
254-1063
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]