RnoINT0084092 @ rn6
Intron Retention
Gene
ENSRNOG00000005678 | Lamb1
Description
laminin subunit beta 1 [Source:RGD Symbol;Acc:1306311]
Coordinates
chr6:50591016-50593080:+
Coord C1 exon
chr6:50591016-50591160
Coord A exon
chr6:50591161-50592872
Coord C2 exon
chr6:50592873-50593080
Length
1712 bp
Sequences
Splice sites
5' ss Seq
CGGGTCAGT
5' ss Score
6.55
3' ss Seq
TTTTGGTCTCTGCTTCTCAGAGG
3' ss Score
7.66
Exon sequences
Seq C1 exon
GTCTCTGAAGCAAAAGTGAGAGCGGACGAGGCTAAGCAGAATGCTCAGGATGTCCTGTTGAAAACAAATGCCACCAGAGAGAAAGTGGACAGGAGCAATGAGGACCTGAGGAACCTCATCAAGCAAATCAGAGACTTTCTGACGG
Seq A exon
GTCAGTAGTGGTTTACTTCTGCTTCAGACACTGGTGTCTGCGAGATTCTGTTTGAGAGGCAAGAAGTCCTGTCTGAGTTGTAGGTAAAGTGAATTTCTGGCAAGAAATAAAATAACAGAAAGTGTTAAGAAATATCTTCATTTCAAACTGAACTTGTAGGTGCTTGTCTGCAATCCTAGTACTTGAAAGGTAGAAGCAGGAAAATCGGGCATCAATGATAAAAAGACTAGAGGAGACCCGGAGCTGCCTTAAGGAAAAATAAAATTGTGTATGCGCATGTACGTACAAAGGTGCCCAGACACCAGAAGGGATGTCAGGTCTGCTGGAGCTGCAGGCATTTGTAAGCTGCCCAAGTGAATGCTGGGCTCCAGACTCTGGTCCTCTGCTAGGCCAGTAAGTACTTGATACTAAGCCCTCTCTGTAGCCCTTCTTTTCTTGAAATAGATGTTGTGAATTACTTTCCAGCACTGCCATACCTGCTGGGTCTGAGCAGCCTATTCAGAAGTCAAAACATTTACTCTGAAAACTGAGTTAGAGTTTCTATCATGGGGATCTTGAAGGAGTTGTTTTCTTTGGCAGTAGCCCCACGGTTTTATGTTCAGAACCTAGCAGTTAGCATTTTCTGTGGAGAAATCTCTAGAGTCTGGTTTAGATTTTTAAGGTTTGTTTATAGCGCACATACTATCACCATGGATATTACTGGTGGAAGACACAGAAAACCCCCAACTGGATCAATTGGTCAAGAAGGGTATTTATGATACCACATAGCCAGGCCAGAAAATAGTGTAATGTCATGGGTCTGGGACTTGCTTTGCCGCATCTCTTGCCAGTATTAAGCCTATCAACTTCATTCTTGATGCAGCCCCATTGTAAGTTGCAGTCTGACATGAAGACAGTGTCTGATGAGGGAAGCGGACCCTTTGAGGAGGATAGAAACCTCTGCCATGCACCTCTGGCCAGGAATTAGTCAGTCCATACATAGATGCCCACTGAAAGTGGGATGTGCCTATAAAAACTGGCAGACGGTGATTTTACCTGATTTTCCAATATTCTGTTAACAGAAAGTTATAAGATCTGCTTTCCAATGATAACTGGAAACAAGATGTGGAAGCCATGACTTGACCATATATTTTCCCCCGCTTAAGTGCTCTGGGGTCCATATTTATGTTTTAGTCAAAAAAAAAAAAAATGAAAACACCTTAAAGAGATCTGAACCTCTGCTGATGGTACAGTCTTGGTTCTTACTGCACTCAGTCCCTTCTAGAATTCCCTAAACATAGGTAACTGATAAGGAATACCAATCCTTTTTTCCTTTTTGAGATAGGGTTTCTATGTAGTCTTAGTTATCCCCACTCACTATGTAGACCCAGCTGCCCTTGGTCTGGGACAACGTGTATAACAACCTCATTAAGTGTAAAGGTTTTTTGTTCCCTTGCAGCTCCAGCTTTAAATGCTGGGCTCTCATCTTCCGTAACCTGAAGCCACAGCTATACATGTACAGTATGCTGTCTGCCCCCTCTGCCTGAATTGTCCTTCAAAACCTGCCTGGTTCCCCATCTTCTGTGATCTCTCCAGCCTACAGCAAACTCTACTGGCACCTCCTTTTCCAAGGGCTTGTCTCTAAATAGCAAGGGTGTGTCTCTTGAGATGGCAGGGGCTTGGCATGTGGCTGAGTGAATCAGCTCTGTGGTGTTTTGGTCTCTGCTTCTCAG
Seq C2 exon
AGGACAGCGCTGATCTGGACAGTATTGAAGCCGTTGCGAACGAAGTACTGAAGATGGAAATGCCTAGCACCCCACAGCAGTTGCAAAACCTAACAGAAGACATCCGGGAACGAGTTGAAACCCTTTCCCAAGTAGAAGTTATTTTGCAGCAGAGTGCTGCTGACATTGCCAGAGCTGAGCTGTTGCTGGAAGAAGCTAAGAGAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005678:ENSRNOT00000008321:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.578 A=NA C2=0.300
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CTGAAGCAAAAGTGAGAGCGGA
R:
TCTTAGCTTCTTCCAGCAACAGC
Band lengths:
342-2054
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]