RnoINT0084074 @ rn6
Intron Retention
Gene
ENSRNOG00000005678 | Lamb1
Description
laminin subunit beta 1 [Source:RGD Symbol;Acc:1306311]
Coordinates
chr6:50551398-50552795:+
Coord C1 exon
chr6:50551398-50551510
Coord A exon
chr6:50551511-50552715
Coord C2 exon
chr6:50552716-50552795
Length
1205 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
TTTAACCGTTTGATCTGCAGCCG
3' ss Score
8.67
Exon sequences
Seq C1 exon
CGTGTGCTTGCAATCCTCTGGGAACAATTCCTGGTGGGAATCCTTGTGACTCTGAGACCGGTTACTGCTACTGTAAACGTCTGGTGACAGGACAGCGCTGTGACCAGTGCCTG
Seq A exon
GTAGGTAACTCCTAATCTCTGAGGATGAGAAGGTAGTGACCATGACATGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTTTTTTTTTTTTTGGTTCTTTTTTTCGGAGCTGGGGACCGAACCCAGGGCCTTGCGCTTCCTAGGTAAGCACTCTACCACTGAGCTAAATCCCCAGCCCCCATGTTTTTGTTTTTGATGTAGGGGCTCAGTATATAGGCAAGGCTGGCTTTGAACTCATAATCCTCTCAACCCTGCCATCTAGGTCCTTGTATGTGCCACCATACCTGGCAAATAAGGAATTTTTCCTATTTATTTTAAACCATCTTTTTTTTTTTTGAGCTGGGGACCGAACCCAGGGCTTTGCGCTTCCTAGGTAAGCGCTCTACCACTGAGCTAAATCCCCAGCCCCAATCATTTTTACATGTTAATGTTAAGAGACCCAAGGGGAAAAGTCAAAATGAGTATTTCTAGTGATTTGCCCAAACTGCATTGAATACTACTTATGAAGACAATCGAACAAGTTTTCTTTTTTTTTTTTTTTAAATGGCATTGCTAACAGCTAGTGAGGACATAATGACTTAGGACTTGTTAACTACTAACAGGAACACAGGTCAACTCTGTGAAAAGTGTTTCAGAGAGACGTCTCAGAGCTAGTAAAAATGGAATATTCCTAACCTAGTGACCGCACTGCATTCCCAGAAGATTCTTGTTGCACCCTTGTTAATTAAGGCAGAAAACTTGTCATCGACAGTGGGAAAATGGTTGCATAAATTCGGGGATTTCCATACAATGTGATATTCAGTTGTGGAAAATGACATTAAAGCAAGGAAGTGTTTACATCGATGTTTTGCATTAACAGATAAAACAGACTTGCAGTGTGAATAACACTTTATGTAGGAAAAAAATCTCATCAAGACAGGCAAAAGTCTGGAGGAAGTACACCAATAATACTGGCCATAATTTATTTCCTGCCAGAGCCATTTGAACGAAGGAAAGTGATCTCTACTGCTCACTCAGAGCCAGGCAGTCCTTTCTCTCACATGACACAAAGTTGAGTTTCTTTAATGAGAATATTCCTACCCTCGGTCTCTTTCCTTGGTTGAAAGAAAGGCTTGGAATAACCCGGGCCTGCTGAAGCTTGTTCTGTGCTGGGTCGCTTGTGCCGTCAGAGGAACCACCTTCTCATGTTTAACCGTTTGATCTGCAG
Seq C2 exon
CCGCAGCACTGGGGCTTAAGCAATGACTTGGACGGATGTCGACCCTGTGACTGTGACCTTGGAGGGGCATTGAACAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005678:ENSRNOT00000008321:12
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=PU(72.0=94.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(24.0=44.4),PF0005319=Laminin_EGF=PU(23.9=40.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGTGCTTGCAATCCTCTGG
R:
TTGTTCAATGCCCCTCCAAGG
Band lengths:
190-1395
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]