BtaINT0084449 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017473 | LAMC3
Description
laminin, gamma 3 [Source:HGNC Symbol;Acc:HGNC:6494]
Coordinates
chr11:101309464-101311185:+
Coord C1 exon
chr11:101309464-101309663
Coord A exon
chr11:101309664-101311038
Coord C2 exon
chr11:101311039-101311185
Length
1375 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGG
5' ss Score
6.23
3' ss Seq
CTGCTGCCTCCCACCAACAGCTC
3' ss Score
9.22
Exon sequences
Seq C1 exon
GAATGAAGCCAAGGTTTCCTCGGCCCAAGGACCAGGCCGCGCTGAGGAGGAAGGCGGCTATCGTCCAGGACAGGATCCTTGCAGACTCGAGAAAGAAGACCAAGCAGGCAGAGAGGATGCTGGGAGATGCGGCTTCTGTCTCCTCCAGGGCCAAGAAGAAGGGCAGGGAAGCCGAGCTGCTGGCCCAGGACAGTGCCAAG
Seq A exon
GTCAGGGCCAGGGATGTGACTCCTGCGGCATCCGTGTCTTCTGGGCCTGGGGGAGGAGTAGCATAGAGGAGGTGCCCTTCTGTGGGGCAGCTGCCCTCACACATTTGCTCCCTTCTGTGTGCAATGCTGAGTACTCTGCACTTACCAGGGGCTCCCAGGCTCTGAGCTCTGGAGCTTTACACGGGTGACCCTGTTGATTTCGCATGAAAGAGATGTCACTGCAGTCCCCATGGGACGGGCAAGGGACCCTGGGGCCAGCCTGGTTCAGTGGCTTCAATCACATGAGCAGGACTCACACCTCGGTGTGTTGGGCTCTACTCCCTAAACCTCTCGGCTTTTCTTGTTTAATTGGGGCCAAATTTGAATTGATGTGAGTCTCCCCAGCACCTTCACTGGCTTTGTTGCTTGGGTCCCAAGTGAACTGCCTTTATTTTTTTAAGTGTATTCTTTTTAAAAAATTAATTAATTTGACTGAATGGGGTGTTAGTTGCAGCACTCGGGATCTTTCATTGCGGTGCACAGACTCTGTAGTTGTGGCACTCGGGCTTCAGTAGTCGTGATGTGTGGACTTATTTGCTCCGAGGCCTGTGGGATCTCAGTTTCCTGACCGAGGATCGAACCCGTGTCCCCTGTTATTGCAAGGCAGATTCTTAACCACTGGGCCACCAGGGAAGTCCCCTAAACTGCCTTCACAGCTGCCTAGAGAAAGTGCTGGATTTGCAGGCGCCCCATGCTTGGTTTCTGGTCCTGTCGTTTCGATTTCAGCCAGCTCCTCTCCTCTGCAGCTCTGATTCCCCATCTGTGAAATAGCTGGAGTTTCTCCTCAGAGGACAGATGGGTAGGGTCCAGCAACCTACACTGTGCCAGCATCCGGTACATACCTGGTGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACCTGGTGAATGAATGAGTGAATGAGCAAACAAATAAATGATCGTGAAGTGATGAAGTGAAGTGATGACCACTTGGCATGATGACCATTAATATCATTTACCTCTAAAAGGACTCTCTTGGGGACTTCCCTGGCAGTCCAGTGGTTAAAACTTCACCTTCCAGTACAGGGGGTGGGAGGTTCAGTCTCTGGATGTGGGGCTAAGATCCCACATGTCTCGCAGCCAAAATATAAAAAAAAAAAATCCATAAAATAGTAGCAATATTGTAGTACATTCAGTAAAGACTTCAAAAAATGATCCACATTAAAAAAACAAACAAACAAACTTAAAAAAGGAAAAGGACTCCTTCCACTCACCCTCCCCTCTCTGCTGCCTCCCACCAACAG
Seq C2 exon
CTCGCCAAGGCCTTGCTGAGGGCAGGGAAGCAGGAACACCGCCGGGCTAGCGGGCTCTCCAGCCAGACGAGGGCGACCCTCGGACTGGCCTCCCGGCAGCTGCTGGCCTCAGAAGCACACAGACAGGAGCTGGAGGCGGCTGAGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017473:ENSBTAT00000023245:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.687 A=NA C2=0.408
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGAAGCCAAGGTTTCCTCGG
R:
CCACTCAGCCGCCTCCAG
Band lengths:
345-1720
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development