BtaINT0084422 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000793 | LAMC2
Description
laminin, gamma 2 [Source:HGNC Symbol;Acc:HGNC:6493]
Coordinates
chr16:65741825-65743987:+
Coord C1 exon
chr16:65741825-65741947
Coord A exon
chr16:65741948-65743797
Coord C2 exon
chr16:65743798-65743987
Length
1850 bp
Sequences
Splice sites
5' ss Seq
CTGGTACGT
5' ss Score
9.57
3' ss Seq
CTTTTTGATCTGTTTCACAGCCA
3' ss Score
8.26
Exon sequences
Seq C1 exon
ATGTTGATGGCTGGAAGGCTGTCCAGAGAAATGGATTTCCTGCAAAGCTCCAGTGGTCACAGCGCCATCAAGATGTGTTTAGCTCCGCACGACGATCAGACCCTGTCTATTTTGTGGCTCCTG
Seq A exon
GTACGTGTGGTGTTTTTCCTGTAGATGTCAATTTAGAAGACTAGGAAGTCAGGATAGAAGAATGGGGTTAGAAAACATGAAAATCTTATCACTTAGTGTCCAGGGCAGTAGCATCTCCAGAAGACAATTGGGGCTTCTGTCCTATTGACAAAGTCATGGCCCAGTAGGGTAGAACTGGGTGTCCAGGTGGTCAGATCCCAGTGCAGGTTCCTGCTTCAGTCAAATGGCAAATTTCTAAGTTTCCCACCAAGACAAGAAATAAGGATTCGGGTCAAATCTGTGGGTCTATCAGGAAGCAGATGGAAAGGTGAAGACAAAGCATTTCTCAAAGCTTTAAACCAATTGTAAATTTTAAAAATATAAAAATCAGAAAAGTTGGATGGGAAAGCTCTGGTTAAAACTTTTTTTAGATTTCTTTTTTTTTTCATGTGGCTCATTTTAAAGTCTTTATTGAATTTAGTACAATATTCCTTCTGTGTTATGTTTTAGCTTTCAATGGCACCCCACTCCAGTACTCTTGCCTGGAAAATCCCATGGGCAGAGGAGCCTGGTAGGCTGCAGTCCATGGGGTCGCTAAGAGTCGGACACGGCTGAGCGACTTCACTTTCACTTTTCACTTTCATGCCTTGGAGAAGGAAATGGCATTCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACGGTGGAGCCTGGTGGGCTGCCTGCCGTCTATGGGGTCACACAGAGTCGGACACGACTAAAGTGACTTAGCAGCAGCAGACCATGAGATTATGTGGGATCTTAGTTCCTTGATCAGGGATTGAACCCACACCCCGTGTATTGGAAGGCAAAGTCTTAGCCACTGGACCACCAAGGAAGTCCTTCTGGCTAGAATTTCTAGTTCATATTCTTAGCTGATATGTGATTCCTGGGCAAGGTGGCCTCTTAACTTTTCCAAACTTTAATTCCCTCAGCTATTAAGTGGGAAGAATAATGACTAACTCCAAGAATTATTGCCACCAAATGTGATGATGTTTGTGCAAGTATTCTATAAACTAGAAAGCACTATGTACCAGATGGTACTATTGCTGATAGACCTGGGAATCTCTACATATTGGTCTGTCATAAGGGCCAACAAAGGTCCATCTAGTCAAAGCTATGGTTTTTCCAGTAGTCATGTATGGATGTGAGAGTTGAACTCTAAAGAAAGCTGAGTGCCGAAGAACTGATGCTTTAGAACTGTGGTGTTGGAGAGGACTCTTGAGAGTCCCTTGGACTGCAAGGAGATCCAACCAGTCCACCCTAAAGGAAATCAGTCTTGAATATTCATTGGAAGGACTCATGCTGAAGCTGAAACTCCAATACTTTGGCCACCTGATGGGAAGAGCTGACTCATTTGAAAAGACCCTGATGCTAGAGAAGACTTAAGGTGGGAGGAGAAGGGGATGACAGAGGATGAGATGGTTGGATGGCATCATTGACTCAATGGACATGAGTTTGAGCAAGCTCCAGGAGTTGGTGATGGACAGGGAAGCCTGATGTGCTGCAGTCCATGTGGTTGCAAAGAGTCAGACATGACTGAGCGACTGAACTGAAGTGATAAGGGCCATGCTGTGAATCATGTAATAGATGGAATTGTCTTATAATGAGGCCCTTTTAGCATTTCATTAACTAACCCTTCTTCATAGTCAATAGCAGTATGGCCATGTCCAGTGCCATGAACTGGCTCTTCTCAAAGAGTAGTTTGTGGGGAGTGATGGGTGAATAATACAGAACTCCAAGAGAAATTGCCAACATCCATGCAAACCTGCTCACTCCTTTTCTTCTCTAGTCCCCCAGCTGATCCTAGTCTTTTTGATCTGTTTCACAG
Seq C2 exon
CCAAATTTCTTGGGAATCAACAGGTGAGCTATGGGCAGAGCCTGTCTTTTGACTACCGTGTGGACAGGGGAGGCAGACACCCATCTGCCCATGACGTGATTCTGGAAGGTGCTGGTCTACAGATCACAGCTCCCTTGATGCCGCGTGACAAGACACTGCCTTGTGGGATCACCAAGACTTACACATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000793:ENSBTAT00000061289:6
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:
PF0005213=Laminin_B=PU(3.8=11.9)
A:
NA
C2:
PF0005213=Laminin_B=FE(48.1=100)
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:
ATGTTGATGGCTGGAAGGCTG
R:
AATGTGTAAGTCTTGGTGATCCCAC
Band lengths:
310-2160
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development