BtaINT0084425 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000793 | LAMC2
Description
laminin, gamma 2 [Source:HGNC Symbol;Acc:HGNC:6493]
Coordinates
chr16:65749992-65751031:+
Coord C1 exon
chr16:65749992-65750210
Coord A exon
chr16:65750211-65750848
Coord C2 exon
chr16:65750849-65751031
Length
638 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GTTCTCCCTCTGCCTCCCAGGAG
3' ss Score
8.52
Exon sequences
Seq C1 exon
GCACTGGGTACCTCGACAACGTGACCTTGATCTCAGCCCGCCCCGTCTCGGGAACCCCAGCACCCTGGGTTGAACAATGTGTATGTCCTGTTGGGTACAAGGGACAGTTCTGCCACGAATGTGCTTCTGGCTACAAAAGAGATTCAGCCAGACTGGGACCTTTTGGCACCTGTATTCCTTGTAACTGCCAAGGGGGAGGGGCCTGTGATCCAGACACAG
Seq A exon
GTGAGTGAAAAGACACCGGGACCAGGCGGTTCGGGGTGCAGCCAGGTGACCGGGGTCTCCTGTGGAAGAGAGAGCTGTGCAGGAAAGGCCGTGCCTGAGCTCATTTCAGAGATGGGAAAGGATTAAGGAGAGCAGGGCTGGACTCCAGGGAAGATGGACACGGCGCTTTATTACATTCCATCCTTTTCACGATGGAAATGCCACAAGATTGTGAGAAAGGTGCTAGGTTACAGGAAATGGCTGTCACGGTTCAGTGCTGGGTCGGGGAGCTGGTGTCACATTGCAAGAATTGTTTGGGGAGATCAAAGGCAGTGTCAGGACCGGAATGAGTATGCCGACAAGTGGTGTAGTCAGGCCGTGGGGAAGAGGGGAGTGGTGTTAACTTATGGATGGTGGTAAAAGGAGTGCGTGTCTGCTTAGCCTGGGAGAGGGAGGGTGAGATTCAGGGTCGTGGCCATGTTTAGAGTTGGCAGGAGGGCAGAGGGGAGGGCCAGCGCTCAGGCACTCTGGGGAAAGCTGCAGACAGGGAGGCTTTGAATTACTAACCCCTGCCTCCCACGCGTCGTCCTCTGTATTAAAGAAAGTGGATAGTTTTACCTGCTCATTTCTCTGCCCTCCGTTCTCCCTCTGCCTCCCAG
Seq C2 exon
GAGATTGTTACTCAGGGGATGAGAACCCTGACATTGAGTGTGAGGACTGCCCCATCGGTTTCTACAACGACCCGCATGACCCAGGCAGCTGCAAGCCCTGTCCCTGTCGCAATGGGTTCAGCTGCTCCGTGATGCCCGAGACAGAGGAGGTGGTGTGCAATAACTGTCCCCACGGCATCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000793:ENSBTAT00000061289:9
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=PD(18.3=32.4),PF0005319=Laminin_EGF=WD(100=51.4)
A:
NA
C2:
PF0005319=Laminin_EGF=PU(52.8=45.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCACCCTGGGTTGAACAAT
R:
TGATGCCGTGGGGACAGTTAT
Band lengths:
342-980
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development