BtaINT0084429 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017473 | LAMC3
Description
laminin, gamma 3 [Source:HGNC Symbol;Acc:HGNC:6494]
Coordinates
chr11:101287389-101289516:+
Coord C1 exon
chr11:101287389-101287607
Coord A exon
chr11:101287608-101289327
Coord C2 exon
chr11:101289328-101289516
Length
1720 bp
Sequences
Splice sites
5' ss Seq
CAGGCAAGT
5' ss Score
3.1
3' ss Seq
GTGCTTGTCTCGCCCCTCAGGGG
3' ss Score
9.63
Exon sequences
Seq C1 exon
GTCCCGTGCTTCTGACTGAGGTCCGGCTCACATCCGCCCGGCGGGGGCTGTCCCCACCAGCCTCCTGGGTGGAGACTTGTTCGTGTCCCCAGGGATACACCGGCCAGTTCTGTGAGTCCTGCGCTCCAGGATACAAGAGGAACACGCCCCTGGGGGGTCCCTATGCCAGCTGTGTTCCCTGCACCTGTAACCAGCATGGTACCTGTGACCCCAACACAG
Seq A exon
GCAAGTCTCCCTGCACTTCCGCCACCCCCAGGCCACCTGGGCTACTCCCAGAGCAGCGAGAAGAGCACTGACCTGAATGTGGCCAGCTGCGTGTGTGTGAGTGATCACTGATACTGATAAGACGGTGTCCTCAAGTTCCTCCATGTGCTAGGCACCTTTTTATAAGCTGTATCGTTGGATCCTGCAAAAAGCCCTGGAGGTGCCAGGACCCTTCCGGTCCCTTGTCACAGGTGTGGGACCTAAAGTGCAGGGAGGCAGCTTGGCCAGTAGGTGGCAGAGCTGCTCCTCTCTCAGGTCACTGCCAGTGACCGTCACCCCCACTTGCAGCAGAGGAAACCCCAGCGGGGAGACCAGTGGCCCTGGGCCGGAGCTGCCAGACTGGGCCTGGACACTGGCCTCTCACATGGGAGGTGGGAGGGCTGGCGCCTTGCTGCTCTTCTGCAGCTTCTAGGGTCTCTGCAAAGGGAAATGCCCTTTCCCCGCTGTCAAAGGACAGTAGCCTGGGAATCAGCAGGCCGGCCGGGGTGGGGGAGCACCCACAGCATGAAGGGCTCCTTCCTCCTGGTGCCCAGGCAGGCATCACTAGTTGAACCAGATGGAGCCTCGTGATCCTTCCATGCGGGGCTCTGGGAGGGTCATCTCATGAGATGGGACTGGTTTGTTGTCCCTCAGAGCCCCTTGCCTTGGCACAACTTCCAGCTCCTTTTGGGCAGGTCTTCATCTGTAAAGGGTGGGGGCACAGTGGTCACTGCGGCCCTTCCTGGGCAGATGGAGGAGTAGTGAGTATGCGGGTGCTGGGCAGAGACAGAGGCCATGGAAAGCACCCCTGGGTGCCCCCCGTGCTCTGCTTGTCCACCCCGGATCCTCTCTCTTTCCTCTGTTCACCCCAGTCCTTGATGAGTGCTGCTAGGGGGGGCGCCTCTGGGAAGGGGTGGTCTTGCTTAACCCCTTCTTAGCCAGGCTCCTCCCTTAGTCCCTGGCAGTGGCTCTGAGCAGACTCTAGACGCCATGGGGCTAGAGAAGGGGGGTTGCAGTGTCCCCTTCATTAGAAACCAGTGGGCAGGAATTCCCTGGTGGTCGGTGGTTAAGACTCCACGCCTCCACTGCAGGGAGCCCAGGTTTCATCCCTAGTCGGGGAACTGAAGATCCGTTGTACATAAATAAATAGAAACCAGTGGGCAGGGAGGGGGGTTCCATTCTGTGAGGCCAAGAAAGCCTCTAGAAACCCACAGACCCCCTAAATGGGTTTCCTCACATTAACGCTGGAATCCTGGGTCCGTGTCACTGTCCCTGAGCTTAAGAGGGCTTGGAGGCTTCAATTTACAGAAGAAAACAAAGAAGCCACTGAGGAGGGGAAAAAGAATACTAGAAGCAAACGCTGGCGGTATCGTCAGCTGGTTCAGTTAATTGTGTGTCAGAGGCTGTGTATGGCTGCACTGAATTGTGATGAAAACCTGTTGAGATCAGAGTCATGTGTGCCCATTTTGCAGGTGAGGAGGTTGAGGCCCAGGGGTGCCCAGCTTCACATGGTCAGTAAGTGGTGGATGTGAACGCAGGTGGATGCTTCATCCCTGGGCCGTGCTGCCTGCACCGTGGAAGAGGCCGCACCCCAGTTCCCACCCCAGGACGTGCTCGGTGGCCCCCACTCAGGAGCCCGCCCGCCATCTTGTGCGGGGTCTGGGTTCAGGTGTGGTGACCAGGTGCTTGTCTCGCCCCTCAG
Seq C2 exon
GGGTCTGCCTGTGTGGCCACCACACCGAGGGCCCGTCCTGTGAGCGCTGCTTGCCAGGTTTCTACGGCAACCCCTTCACAGGCCAGGCCGACGACTGCCAGCCCTGCCCGTGCCCCGGACAATCGGCCTGCACGACCATCCCAGAGAGCGGAGAAGTGGTGTGTACCCACTGCCCGCGGAGCCAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017473:ENSBTAT00000023245:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.054 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005213=Laminin_B=PD(18.2=32.4),PF0005319=Laminin_EGF=WD(100=50.0),PF0005319=Laminin_EGF=PU(26.5=17.6)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(71.4=54.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCTGACTGAGGTCCGGCTC
R:
CTCTCTGGGATGGTCGTGCAG
Band lengths:
358-2078
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development