GgaINT0124020 @ galGal4
Intron Retention
Gene
ENSGALG00000003852 | LAMC3
Description
laminin, gamma 3 [Source:HGNC Symbol;Acc:HGNC:6494]
Coordinates
chr17:6071617-6073030:+
Coord C1 exon
chr17:6071617-6071838
Coord A exon
chr17:6071839-6072841
Coord C2 exon
chr17:6072842-6073030
Length
1003 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGC
5' ss Score
9.1
3' ss Seq
CTCCATTTCTCACCTCACAGGGC
3' ss Score
8.92
Exon sequences
Seq C1 exon
CAGGCAGGCTGTGGCTGAGCCGGGTGCAGCTCACGTCAGCTCGCCGCGGTGCAGGCATGCGGGCAGGATGGGTGGAGGAGTGCACATGTCCTCCCAGCTACGCTGGGTCCTTCTGTGAATCCTGTGCACCTGGCTTCAAGCGGGACATCCCCTTTGGTGGCCCCTTTGTCACCTGCGTGCCCTGCACCTGCAACCAGCATGGGGACTGCGAGCCGCTCTCAG
Seq A exon
GTGCGCACCCGCTCCCTCTGCTTGCTGGATCACAGTGTGCACGGGGAGCACATCTGTGTCTTTGCTTATTCTGAGGAATGCTGGAAACCATCCTGGAGGTCAGGGAAACACAGAGCAGAGGCTCAGAGATGCTGCCTGGCTCCGTGTGCATCCCTACAGCAAGCAACAGCACACACTGGTGCTGGGAAGAGATGGAGATGAGGTGATGTGTGCAGTACCCAGATGGGGCCCCTGGCCCGGGCACGTGGAAAGGAACAACAGAACTTTATGGGCAGAGTGGGAAGGGCTGGAGGAAACATTTTGTTCAGCGTGTGCCTCTGCTCTGCCAGCAACACACGACACCGGGCTGCAGACAGCCGGCATCTCGCTGGGACAGGGCTGAGCCCTGGGAACTGGGACAGAGCTTTGTTGTCCTGGCCCCTGCACGGTTTCTTTCCACTGCATTTCCCCCCCCCCCCCATTTCTGCCATCTGCTTTTCCTTTGCTTGCCATTGCCTGTCTCTGCCTCAACGTGGGGAAAATGGAAACATGCCCATTCCCTCCTGCACGACCCGCCTGCTATCACCTGACCCCCCCCTTTTCCCCTTCCATTCAGCAAAGCATCTGTGTGGAGGCGGGGGTCCTTGAGCGTCCTTCCTCCTCCTCCTCCAGCTCCCAGCTGACTGCGGACGGCTGTGACTCACCAGCTCGGCTCGAGGAGACGCTCGCTCCCCGCTGGGTCACGGCCGCCCGCTTGTGTTTTCCATCCCAGGCTGGGAGCGCGGCAGCTCGGCGCTGGGAAATGTGTTGCCCATTACTGCAGGCGCCGGCAGACTTGGGGCACGATGCTGGGGCTGCCTGCACCCACCTCACGCCTGCACAGCATCCTCCTCCTCCAAACAAGAGCCGGGCAAGAAGGAGGGGGGGGGAAGTGTGACTGGCTGCTTTAGGAGCACACCAACACTGTGGCTCCTTGGAGCTGCATATCCGTCCTGGCAGCACATCTCCATTTCTCACCTCACAG
Seq C2 exon
GGCACTGCCGCTGCTTGCACAACACGGAGGGTCCCTCCTGCGAGCGTTGCAGCCCCGGGTTTTATGGCAACCCCTTCACTGGGCACCCCGATGACTGCAAGCCTTGCCCGTGCCCTGGCCGCTCACCCTGCACTCAGCTGCCCAGCAGTGGGGAGGTGGTGTGCACCCACTGCCCCCCGGGGCAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003852:ENSGALT00000006123:13
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=PD(18.7=33.3),PF0005319=Laminin_EGF=WD(100=41.3),PF0005319=Laminin_EGF=PU(28.3=17.3)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(69.6=50.0),PF0005319=Laminin_EGF=PU(52.8=43.8)
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:
GGGTGCAGCTCACGTCAG
R:
GCAGCTGAGTGCAGGGTG
Band lengths:
342-1345
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]