BtaINT0084285 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011412 | LAMB1
Description
laminin subunit beta-1 precursor [Source:RefSeq peptide;Acc:NP_001193448]
Coordinates
chr4:49313421-49315528:-
Coord C1 exon
chr4:49315408-49315528
Coord A exon
chr4:49313610-49315407
Coord C2 exon
chr4:49313421-49313609
Length
1798 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
ACGTAGATCTTGTTTTGCAGAGT
3' ss Score
6.64
Exon sequences
Seq C1 exon
GTTCACGGACACTGCATGTGCAGGCATAACACCAAGGGCTTAAACTGTGAACAGTGCATGGATTTCTACCATGATTTACCTTGGAGACCCGCTGAAGGTCGAAACAGCAATGCTTGTAAAA
Seq A exon
GTAAGTCTCAGGCAGGGAATTCCCTGGAGGTCCAGTGGTTAGAACTCCAAGCTTTCACTGCCAAGGGTGGTGAAAGTCCCTGGTTGGGAAACTAAAGTCCTGTAAGATATGCAGTGGTACCAAAACAACAAGAAAAAAAGAAGTAAGTCTTAGGCAAAGGGATGTTTTGAATCAGTTCAGACCCCAGGATCCATTTTCTGAGTAGACGTGCTATAATAGTACACTATTTTGCAAAAGGAAGAAAAGTTACTACCCTTTTCCCAGCCTCGCCCTAATACTCCTAGGAAGCCATTATCCACTCAGATTAATCAATTAGCATTTATTAAGCAGCTCCCATGTGTTTGGCAGATGTTGTGTGCCGCCTGTAACATTGCACTTTTTTCAAGGCCAGATGACTGAGAAAAATGAATGAAAACGATGTTGTGGTGGATCCATAAGGTCTAAGAGAGATGGAGTACTTGTCAGCCTTGTTCTGTGCCAACCCAGGTGCCGCCTGTGGCCTCCTTCAATCCATCCATCTGCCATCCCTCCTGGTGCTATTCTCTGGGCAGAGGGGAAGTTTGAAAACCACCACCCTCCCCACCTCACACAGTGATGCTGATAGATGATCATCCCTGCAAACGTGCCTGCCTCTGACCCCACTGAGGACAGAGGGGTTAGGAGTTCAGAAACCAGTGAGGGCTGGAGTGGTCAAGGTTTTTGTTAGTAAGGACAACTAGCTGGGCCCTAGCAAGTAGTTAGGATTGTTTAGATAAAGAGAAGAAAGCAGGGGGAAGGTGGAAGGGAGTTCAGATAAGGAGAATACAAAACACAAGGCTCCTAGGACCTTCTCATGATATCGTGGTTTAATTCATGATTCCATGGTTCCAGGGTTTAATCAAACCAATGCATCCAAGGCAGGATGACACAGTCCCTCCCTTTAGGATGGATAAGACCAGTTGTAGAGCCCTTTGAGAACCCAGTTGAGTTAAGCTTCCTTGTGAGAAGACAAGAGGAGTCGATGAGGATAGCTGAGCACGAGAGGGAGACGGTTAAAGCTGGGTTGGACCAAGAGGACTCTGCCAAACAGGCTAGAGGAGAAACAGACTGACCCAAGAAGACTGGCTTGATGGCTGTTAAGGGTCTGATTCATAGAGCCTGGCCTAGGGTGGTGGTAGGAACGGGGAAGAAGAGAACGCAGCCTTCATACCATGTTCCTCAAAGCCAAGAGCCCAGACAGGCTTCCCCAGGAACATATCGCCTAGAAAACCCTCTGGAGTGATGTATTCCTGTCCTACTCTGCACACAACCCAAACGAGTCCTCCATGCAGTGCAGCCTTCCTGTGGGTGAGCCTGTGAGGGGACTTCCCTCAGAGCTTTTACACTTTTTATAGCCCATTCTCTTCCAAAGAGGGCAAATGAGGTTATTTCATAAAGATCACACTTGGAAGGTTTCCAGCATGGTTTAGGATTTAAACTGATGGCATAAGCAGATGTATTTTTTCCACCGCCAGTTCCTTCTTGTTAGTTGCCGTTTTGCCTGACTTCATCCCCAGTTTCCAAAATGAGCTTCCTTCCCACCAATCCCATCCTCCACTGGTTTTTCTTGTTCAGTCCCTTAGTTGTATCTGACTCTTGGTGACCCTGTGAACTACAGCATGCAGGGCTTCCCTGTCCTTCACTGTCTCCCAGAGTTTGCTCAAAATCATGTCCATTGAGTAGGTGGTGCCATCCAACCATCTCATCCTCTGTCGTCCCCTTCTCCTCCACTGGTAAGTAGATTGAAAAGATTTTTCCTGACGTAGATCTTGTTTTGCAG
Seq C2 exon
AGTGTAACTGCAACGAACATTCCAGCTCATGCCACTTCGACATGGCGGTCTACTTGGCCACTGGCAACGTCAGCGGAGGGGTGTGTGATGACTGTCAGCACAACACGATGGGGCGCAACTGTGAGCAGTGCAAACCGTTTTACTACCAGCACCCGGAGAGAGACATCCGAGATCCTAGTCTCTGTGAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011412:ENSBTAT00000015166:8
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:
TGTGCAGGCATAACACCAAGG
R:
GTTCACAGAGACTAGGATCTCGGA
Band lengths:
294-2092
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]