BtaINT0084257 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011412 | LAMB1
Description
laminin subunit beta-1 precursor [Source:RefSeq peptide;Acc:NP_001193448]
Coordinates
chr4:49311277-49312835:-
Coord C1 exon
chr4:49312723-49312835
Coord A exon
chr4:49311357-49312722
Coord C2 exon
chr4:49311277-49311356
Length
1366 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
TTTAATCTTTTGTTCTGCAGCCA
3' ss Score
8.71
Exon sequences
Seq C1 exon
CTTGTGCTTGCAATCCTCTGGGAACGATTCCTGGCGGGAATCCTTGTGATTCTGAGACCGGTTACTGCTACTGTAAGCGTCTGGTGACAGGACAGCATTGTGACCAGTGTCTG
Seq A exon
GTAGGTAAATCCTAATTACATGGGATGGGTGGTTTGTGAATGTGTTCCAGTAGAGAATGATTTTCACAGTTGTTTTGTAGGTTCTGCCTACAAAACACCCTTTTATGTAAATCATAAAAGCCACTCGTAGACAATTCACAAAAGAGAAATTACTAATGAATAATTTTGTCAGGATATTCACCATTACTATTAGAACTGTAAAATAAAACCAGAGTGAAGTACTGTTTTTACAGACAAAACTAACAAGTTTTTTTTTTTAATGGTAATGCTGACTAATAAGTGAAGTCATAGTGAGAGGCTGGTACTCGAGTGCTGGTGATGAAAATACAGATCGGCTCATACTTTGCAAAAAGCATTTTGGAGATGTGTACCCATTGCCTGTAGAAATGTGCATACCCTTTGACCCAGTAATTCCACATCTGGGGATCTATCCTAATGAAATAATCAGAAAATTGGTCAAAGATGAATTCACTAGAAGACTCATAGCATCTTTTATCAATAGCAAAAAACACTTGGAAGCAACAGTAGGGAAAATATTTAAATAAATTTGGGGGTTTCTATACAGTGTGATGGTTTCCCTGCTGGCACGGCAGTAAAAAAAAATCCACCTGCCAATGCAGGAGATACCAGTTTGATCCCTGGGTTGGTAAGATCCCTTGGAGGAAGAAATGGCAACCCACTCCAGTATTCTTGCCTGGGAAATCCCATGGACAGAGGACCCTGGTGGACTACAGTCCATAGGGAAGCAAAGAGCTGGACAGGACTTAACAACTAAGCAACAACAAAACAGTATGATATTTTGTTGCTATTGAAAATGACGGTAACACAAGGGGGAAATGCTTATGCTGGTGTCAAAAAAAGCCACAGGATGTGAGTAGTATCTTGATTATGTAGGGAAAAAGTTCATCAAGAAAAACAAAATCTGGAAGGAAGTAGACCAAAAGTTCACTATGGTGATCTGGAGAATATTTATGAAGGTAATTTTTTAAATTATTTTATGTCTTTTATAACATTCTTGTGATTGCTTTCATAATTACTGACTTACTGCCAGAGTAATTCTAAAGAAAATTGGCATATTTGCTGCCAGCTCATGTTAATTTTTGGATGAAGGTTACTTGCAGGGCAAAGAAACTGCTCTGATCTGGGGTTACCATGTGGCTATGTGCAATCTTCTCTGACCCCAGTGACCTGCAGCTTGCGGTTCTCTATTCTAGAACACTCACGCCTCGTGTAGGCTTTCTGCTTTCACAGTGCAAAAGAACGTTTGGTGGAACGTCGTCCAAAACACGCCATAACTTGTCTCTTGCTGGGTCTATTGTGTAATTACAGGAACCCCTCTTTAGATGTTTAATCTTTTGTTCTGCAG
Seq C2 exon
CCAGAGCACTGGGGCTTAAGCAACGACTTGGATGGATGTCGACCTTGTGACTGTGACATTGGGGGAGCCTTAAACAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011412:ENSBTAT00000015166:11
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=PU(72.0=94.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(24.0=44.4),PF0005319=Laminin_EGF=PU(23.9=40.7)
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:
TTGTGCTTGCAATCCTCTGGG
R:
ATTGTTTAAGGCTCCCCCAATGT
Band lengths:
190-1556
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]