BtaINT0084093 @ bosTau6
Intron Retention
Gene
ENSBTAG00000027181 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:HGNC:6483]
Coordinates
chr24:33174429-33176253:-
Coord C1 exon
chr24:33176113-33176253
Coord A exon
chr24:33174591-33176112
Coord C2 exon
chr24:33174429-33174590
Length
1522 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGC
5' ss Score
10.4
3' ss Seq
GCCTTGCCTCTGTGTTTCAGCTT
3' ss Score
9.69
Exon sequences
Seq C1 exon
GAAAACGTGCAAGGCACAGAATGCAACATGTGTCGGGAAGGGTCATTCTACCTGGACCCAGCGAATCCCAAGGGTTGTACCAGCTGCTTTTGTTTCGGAGCCAGTCATCACTGTCACAGCACACTTAAGAGAAGGGCTAAG
Seq A exon
GTACGCAGGGCATCAGAGTCCTTCTGTTTTTCTTTAGCACTTCTAAATGAGGAAGTGAGGGGTTCCCAGGTGGCACCATGGTAAAGAATCTGCCTGCAGAACAGGAGACGTGAGTTCAGTTCCTGGGTTGGGAAGATCCCCTGGAGTAGGAAGTGGCAACCCACTCCAGTATTCTTGCCTGGAGAGTTCCATGGACAGATGAGCCCAGTGGGCTGCAGTCTGTGGGGTCGCAAAGAGTCGGACATGACTGAGCATGAGCACGCATAAAAGAAAAAAATGAGAAAGTAATGCACTGGCATGAGAAGTGAACAGTCATGGAGGTTTTGCATCCTGCTGGGTTAGAATGTTAAGCCCTATGCTCACTGTCGTTAGCCTGCAGCGTTCTGTCCCCAGATGTCCTCATGTCCCTCAGCTCACACCCCTCATCAGGTCTCTGCTCATGTGTCCCAGTGCTCGGAGAAGCCTCCCGTCACCACTCGCTGACTCTGTGACCTCGCCTTTCTCTGTGGACTTCATAGCGTGCATCACAGTTCTAATGCTTATTATCTCTCTTCTTTCACCACTTGCGTGTAACCTCCTTGATGGAATCCCAGCACCGTGAGCAGGATCTGAAATGTAGTAGTTGCTCAATAAACACTCATTAGAGTTGCTTGTTCTCCTCCCTTACTTCTTATGTGCTTATCTTCCTGTTTTACTTTTCTTCTCACCTGTTTTACCACATCTTGTCTTTGGTCACTCTTAAAATCAACTCCAGAAAGCTAAAGCTTGTGTTGCCTCCATGATCCCACGCTTGCTTGCTTGTGTGAGTCGTGTATTTGTTGTTGTTGTTTAGTCGCTGAGTTGTGTCCGACTGTTTTGTGACCCTATGGAGTGAGTCATGCATTATGTCCAACAAATGTTCAAAGAAAGATTTTTGTATCTGTTTTACTGCTTGCCTCCTGAAAGGAGCACAAGCTTGTAGTGGGGGGAGAAAGTTATTTTGTAAATCCACCCTAAAGGCTCCTCTTCTTATCCCCAGGGGACCCCCGAAGCATTATTCCACATCTATGCCTTGTCAGCTCCTTCTTTTTCTTCCCCTCATAATTTAACTCCTGGCTTCCTTTGTGATCAGGGGAGTATTTAATTCTGATGCTCCATTTAGAGAAAAACAACGACAGCAGGCCACTGTACTTCACATCACATTTTCTCTCTGAGGAGCTCACCATTAAAATGCGCCCACAATCCTAGTTATGATCCACACCCTTATTTGCATATTATTCGAACAGTTATTGGACACCTACTAAATGTCAGGATGTGCGCAGGGCTAAAGGATAAATCCCACGTACATATGGCCACTATCCTTTGAGAATTCCTAGTCTCAATTGGTCAGTTGGGGGCTGAGCGGGAGTCAGAGACGAGGAGACACCCGAGGGAGGCCTTTGCAGCAAGGTGGCTGCCCCGTGGCTCTTTCTGCTCTTCAAGATTCAGCCATCACCAGAGGAGCCACAGGCATGTGGTTCCATGCCTTGCCTCTGTGTTTCAG
Seq C2 exon
CTTGTGGACATGATGGGCTGGCGCCTGCAGACAGCAGACGGAGTGGACATCCCCGTCTCCTTCAACCCCGGCAGCAGCAGTGTGGTGGCCGACCTCCAGGAACTGCCCGCCACGGTCCATAGCGCGTCCTGGGTCGCCCCGCCTTCCTACCTGGGGGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000027181:ENSBTAT00000060991:33
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(51.0=53.2)
A:
NA
C2:
PF0005213=Laminin_B=PU(8.1=20.4)
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:
AGAATGCAACATGTGTCGGGA
R:
CTTGTCCCCCAGGTAGGAAGG
Band lengths:
286-1808
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]