RnoINT0084103 @ rn6
Intron Retention
Gene
ENSRNOG00000005678 | Lamb1
Description
laminin subunit beta 1 [Source:RGD Symbol;Acc:1306311]
Coordinates
chr6:50549087-50550822:+
Coord C1 exon
chr6:50549087-50549207
Coord A exon
chr6:50549208-50550633
Coord C2 exon
chr6:50550634-50550822
Length
1426 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
ACATTGGTCTTGTCATGCAGAGT
3' ss Score
7.07
Exon sequences
Seq C1 exon
GTTCATGGGCACTGCATGTGCAGACACAACACTAAAGGCTTGAACTGTGAGCTGTGCATGGATTTCTACCACGATTTGCCGTGGAGACCTGCCGAAGGTCGGAACAGTAACGCCTGCAAAA
Seq A exon
GTAAGTGGCAGTGGTCAGGCTGTTGGAGGCAGGGGGTCCATTTTCTGGGGAGCTGTGGTCTTTGATTACACTGTTTGCAGAAGGGAGGGGCATTGTGCTATTCTCCTAGCTGTGTCTGTCCCAGAGCAATAATATGTATGCACTGGGGTCAAGTAATAAAAATTAGTGTGTTTGGCATTGACTGGGGAAAATGGCAATGGTGTCGTGACTTTATATTTGCTTTTAAGACAAGAGAACGACAGGGCAAGTGAAAGACAGCTACAGTGCCTTTCATGCACTTAGCTGGTTGAACTATTGAGAAGTAATTGGGTCTCCAAAATACTCGATCAGTGGGTTAGTTCAGTGATGAGTTCCTAGCTGACTGGTTGACTGGGTTAGGCCCACCTAGAGGAGGTGCTTCTCAGAGGTCCGCCTTTGATGCTGCTTCTTCTTCCCAACCCCTTCTGATTGTTCTTCTGCTCCCTGACTGCGATTCCATGCCTTTCTGCCATCGCATTTGGCCTTATCACAGAGCCAGCAACGAGAGCTGGCCAACTGTGGACTCCAAGGAAACCCTCCTTTAAGTCGTTTTCCTGAAGTGTTTGGTCACGGGGAGGAATGAAGTCTGGCTCATTGCCAAGCTGCCCACATGCCTGAAATACAGGGTGTGTTACCTGCCTGCCACTGTCATCCCCGCACATCCTGTCATAGTCTTCCGATAGCCAACCCAAAAGGCTTTTCTAGGAATCCATCAACCAGCACATCCTTTAGAGTAGAAAGTCAATCAGTTTCTTCCCTGGGTGGGGCCAAAGCTACCTTCAGCGGTGGAATGGCACCCCTCCTCCTGTGTTGGTCACTTTTCATAACATAGCCAAGTAAATCAACATAAAATGGGAAAGATCCGTCAGACCACGGTCACTTGGCTGTGCTGCTTCAGGTCTATGGGAAAGCAGAAGCATCGTAGAAGACAGTAGAGTAAAGCTGGGAGAAAGACAGCTTTTGGAGGTCACCCCAAGGACTTACTTTCTCTAGGCAGACTACACCTCCTAGTTCCCACTGTCTTCCAGTAACGCCATTAAATTATGAGTCCACCAGGGGATTAAGCAACCCACGGACCAGGGCCTTCATGATCTGGTTATTTCCCAACCCAGCCTTTTAAACATGAACCTTGTCCTATTATTCCTAGGGGATTTTTGTCCAAGACTTTCCTGTTTATGATAACAGTATTTATTTATTTTAATTTTTGAGAAAGGGTTTCTCTGTGTAGCCCTGCCCATTGAAACCTCAAATCAGGTTAGCGTCTTATCACCAGAGGCTTCTCACTGGTTGGCTGCTATTTCACTCAGACTCACTCCCCACTCTGTTCAGTGAGCTTCCTTCCCGACCCCTCCGTCCTCCGTTGGTAAACAGATTTAAAATTCTTCTTGACATTGGTCTTGTCATGCAG
Seq C2 exon
AGTGTAACTGCAACGAACATTCCAGCTCGTGTCACTTTGACATGGCGGTCTTCCTGGCTACCGGCAATGTCAGCGGGGGAGTGTGTGATAACTGTCAGCACAACACCATGGGGCGCAACTGCGAGCAGTGCAAACCCTTCTACTTCCAGCACCCTGAGAGGGACATCCGGGACCCCAATCTCTGCGAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005678:ENSRNOT00000008321:9
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=PD(61.3=92.7)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=95.3)
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:
GTTCATGGGCACTGCATGT
R:
GTTCGCAGAGATTGGGGTCC
Band lengths:
310-1736
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]