RnoINT0084082 @ rn6
Intron Retention
Gene
ENSRNOG00000005678 | Lamb1
Description
laminin subunit beta 1 [Source:RGD Symbol;Acc:1306311]
Coordinates
chr6:50529036-50530450:+
Coord C1 exon
chr6:50529036-50529157
Coord A exon
chr6:50529158-50530274
Coord C2 exon
chr6:50530275-50530450
Length
1117 bp
Sequences
Splice sites
5' ss Seq
TAGGTAACT
5' ss Score
6.43
3' ss Seq
GTTGCTTTTCTCTTCTGTAGCCC
3' ss Score
8.82
Exon sequences
Seq C1 exon
AAAGGAAGACACGAAGAAAAGACGGGCAGCTTGCCTGCCGCGTCCTCCTTCCCGTGCCGCGTCCCCTCGCCTGCAAGGACTGGACATGGGGGTGCTCCAGGTGTTCGCCTTTGGTGTCCTAG
Seq A exon
GTAACTCAAGCTAAGGGTTGGGGGGAGGGGTGTGCTCGGGCGGTGGGGGAAAAAAAAACCCAAACCGGTTTTGCCCCGGCATTGAAGGAATCTTGGGGGGTCGGAGGAGAGAGAGGGTGGTTGGAAATAACGCCGTGGGATCGATCGCCACCGCTCTCGCTTCGGTGGTGGCTGGGGACCGCGCACGCGGAGCTCCGCGGACCCGCATCCCCTGGGTTTTGCGCACAGAGCTCGCGCTCCTGCTGGCTTCCGAGGCTATTGCTCCGGGGCTTTGCACATTTACCAGTTAAACGCTGTTTCCCCTCCGTGGAAGGCATGCTCCCTGGTGTGGCTGGGCAGGCAGCGAAGGGTCCTGGAAAAACCAATTACGCACAAAAGTGTAGGGGCCCGGAGCAGGCTTCGACTTGGGAACAGATTGGGGCCATGTGGCTTTAATTAACCATCCTTGTTTGTCTCTGGGTGGCACCACGAACAGTTGGGCCGGGTGCTTTGCTGGAATGGCGAAGCGTTGAAGCCACTACAGAGCTACAGAGACACACCAGCGGTCTCTAGCTCATGGAATCAGCTTCTGTGGCAAACACTATGCCTCATCCCGGCGCTATCGCTGGTGACCCTGGCACGAGCACGCGGACATATTTTTGTGCCTCCACCCCACCCCCATCCCACAGATTTCCCACACACCGAGGATGCACCTACTGCCGCTTGCACGCCGGTTCTCCTTAGCGAATGTGCTGCGTGTGTCGGTGTCAACCTCACTGTGCCCTGATCTAGGCACGTCGAAGTGACTGGGTCACTACGTCCACCTTTCATAGAGAGGCTCTGCTCGGCTGGGGCAGATCAGAGTAGACAAGAGAGTCAGTTGGATTTCCTTGGTGCTGCGCTCAGCTGACGACTATTAGTCAAACCTAATGACTAGTCTGGGGTACCCCCCCCCCCATCCTTCTCTCCTGGTCCCAGCTTTCCAGGCCTCTTCTGCGCCTATCTCTCCATTGTGTTTTTCTATGTATTCTTTCTCTTGAATCCTCTGCCTGCCCCTCCTGCTGTTTTTCTTTTGCTCTGGCTTGTCCGTTGCTTTCTTCTCCCTTCCTCCTAACCTTGTTGCTTTTCTCTTCTGTAG
Seq C2 exon
CCCTATGGGGCACCCGAGTGTGCGCTCAGGAACCAGAGTTCAGCTATGGCTGCGCGGAAGGCAGCTGCTACCCCGCCACTGGCGACCTTCTCATCGGCCGAGCTCAAAAGCTCTCAGTGACCTCGACATGCGGACTGCACAAACCAGAGCCCTACTGTATTGTCAGCCACCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005678:ENSRNOT00000008321:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005512=Laminin_N=PU(15.3=61.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAAGACACGAAGAAAAGACGG
R:
GCAGGTGGCTGACAATACAGT
Band lengths:
294-1411
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]