BtaINT0084255 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011412 | LAMB1
Description
laminin subunit beta-1 precursor [Source:RefSeq peptide;Acc:NP_001193448]
Coordinates
chr4:49338561-49339822:-
Coord C1 exon
chr4:49339750-49339822
Coord A exon
chr4:49338737-49339749
Coord C2 exon
chr4:49338561-49338736
Length
1013 bp
Sequences
Splice sites
5' ss Seq
TAGGTAATT
5' ss Score
7.27
3' ss Seq
TCCGCCTGCCCCTTCCACAGCCC
3' ss Score
9.07
Exon sequences
Seq C1 exon
TCGGTGGCCGTGTCCCCTGGGCTGCAGGGACTGGACATGGGGCGGCTCCAGGTGTTCGCGTTCAGTTTCTTAG
Seq A exon
GTAATTCAGAGGAAAAGGGGCGCGGGGTGTGTGTGTGAAGGGGTGGGCTTGGAGGAAGAATAACCAAACCGTTGGACTCAGCTTTGGGGGAAGCCTGTGGGAAGAGGGACTTGATAGAAATCTGCTTTGGGATTAATCGCCAGCGCCCTCGGTGGTGGCCGGGGACCGCATCCTGGGGTGTTTGTGCCCAGAGCTCCGGGTGCTCCCGCAGCTCCCGCTCTGGGCTTTGCGTCTCCGGCCCTTTTTCGGTGGGACTCTCCATCTCTGGGGTCAGGCTTCCTGGGCTCTGGGGTCAGGCTGCGAGGGCTCCTCAGAAGCCCATCCGGGAGAGTGCCTGAGCTGAGTGCAGGCTTCATCCTGGGAACAAATTGGGGCCATGTGGCTTTAATTAACCATCGCTGTTTGCCCCCGGATGGCGCCAGAAACAGCTAGATCGGGAGCTTCTCTGGAATGACGAATCGCTGAAGCCAGTCAAAAGCCTCAGGGATTGACCACTCGCCCCTTGTTCGGGACAGTGGTGTTCCCCGCGAACCCCATGATCCCCCGTCCCCGGCGAAGCGTAGGCGACCTCCGAGTGTGTGGGCACACACACTCACGCGTCCCCACGCTTACAAATTTCCACGCACACACTTGCACTGTCACCCAAGGATGCACAGGCTACCGTGTGCGTGCGAGTTCACATACTAGTGGGTGTGCGGCGTTTGGCCGCCTGCGTCCGGGTCCAGGAACCTCGTAGTGACCGGAGCTGCTTCCCAGGGCTGATCAGGGTGGGCGCGAGAGTAGGTGGGCTTCCTAGGAGTGATGCTCTCAGTTACTGGACAAACCTGCTGTATCTGTTTCTTTCTGAATCCTTCTCTCCACGTTCTGCCTTCCCGGCCTCACTCCATTGTGTCTCTTTCCTGTGTATCTTGCTTTTTTCCCCGAATCTACTCTGTCTCCGCCCCCTGCTTATTCTCTTTGCATGGGCCCGCTCCCTGCTTGTGCCCTACGCTGTCCGCCTGCCCCTTCCACAG
Seq C2 exon
CCCTGTGCGGAGTCGGAGTGAGCGCTCAAGAACCCGATTTCAGCTACGGCTGCGCTGAGGGCAGCTGCTACCCGGCCACAGGCGACCTTCTCATCGGCCGAGCGCAGAAGCTCTCAGTGACCTCGACCTGCGGGCTGCACAAACCCGAGCCTTACTGTATCGTCAGCCACCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011412:ENSBTAT00000015166:1
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
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTCCCCTGGGCTGCAG
R:
TGGAGGTGGCTGACGATACAG
Band lengths:
239-1252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]