GgaINT0011793 @ galGal3
Intron Retention
Gene
ENSGALG00000005321 | LAMA5
Description
NA
Coordinates
chr20:7826185-7827074:-
Coord C1 exon
chr20:7826844-7827074
Coord A exon
chr20:7826299-7826843
Coord C2 exon
chr20:7826185-7826298
Length
545 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
TCCTTCTGCTCTCTCCTCAGGAA
3' ss Score
12.44
Exon sequences
Seq C1 exon
AGTAACTTCAGGCACACGGAGACACACAACCCTGTATCGAGAGAGGAGCTCATGATGGTGCTGGCAAACCTGGAGCAGCTGCAGATCCGGGCACTCTTCTCCCAGCTCTCCTCCTCCGTGTCCCTGCGTCGTGTGGTCCTGGAGATTGCAACAGATACAGCTACAGGTGTCCCCGCAAGCAACGTGGAGTTGTGCTTTTGCCCAGCTAACTACCTGGGTGACTCCTGCCAG
Seq A exon
GTAGGAGCATGAGGAGCTCACGCTATTTAGGCAGAGAGCGGTTGAACAGCTGCAGACAGACACCCCTCATGCTTGCTGCAGGTGGCAGTCTGTGGGTTTTGGATCACTGAGCAGAGCAGTGGTGCCACACAGTCTGCTTGCAGGCCAACCCCTGAGGGTTTTAGCTTTGATCACAGCTCAGGTTGTGCCTGAGGAAGAAACAGCATCTCCCAAACTCCCCCGCACCGACCTGCTCACAGCTTCACTCCTGCCACAGCACAGCACAGCTGGGGGATGTGTGCCAGCTGCATCTGGCCTCTTGGAGGGGACATACTGGGCAAATTTGTTGAAGACCTAAATCAAGTTTGTGCAGTACCTTGAAGGAGATCCTCTGCCTGGCCAGTTCTCTCTTACTGATGAGGAATAGAAAATCTTTGTTGTTGCTTTTAATCTCTTCTCCTTCAGTACAGCCCAGTGGGGATTCTGTCATGGCTATTAAATGGGTCTGTTTGCTTTGTCTGAATGTTTCAGGCTCTTTTTCACATCTCCTTCTGCTCTCTCCTCAG
Seq C2 exon
GAATGCGCTCCAGGTTACTACAGGGACACCAAGGGGCTATTTTTGGGGAAATGCATCCCATGTCATTGCAACGGCCACTCAGACCAGTGCCTGCCAGGGTCTGGGATATGCCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005321:ENSGALT00000008535:42
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(45.3=80.5),PF0005319=Laminin_EGF=PU(48.6=23.4)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(45.9=44.7),PF0005319=Laminin_EGF=PU(35.4=44.7)
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:
AACTTCAGGCACACGGAGACA
R:
AAGGCATATCCCAGACCCTG
Band lengths:
342-887
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]