BtaINT0084074 @ bosTau6
Intron Retention
Gene
ENSBTAG00000027181 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:HGNC:6483]
Coordinates
chr24:33243870-33244837:-
Coord C1 exon
chr24:33244732-33244837
Coord A exon
chr24:33243970-33244731
Coord C2 exon
chr24:33243870-33243969
Length
762 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
AGCCGTTTCCTGACTCTCAGGGT
3' ss Score
6.73
Exon sequences
Seq C1 exon
TTAGATGGTGACTGTCATTGTAAATCCCATGTTGGTGGCGATTCCTGTGACACATGCGAAGATGGATATTTTGCTTTGGAAAAGAGCAATTACTTTGGGTGTCAAG
Seq A exon
GTAAATTCTCCCAGAGGTTCCTGTGTAAGGCAAAAATGTTGATGGGCAAAGACTGTCAGAGTAACCTTGCTTCTGAGTTCACTGTCTTCTTGCTGACTTTCTGATAGAATGGGACTGAAAAGTCCTGTCTAGGGAAATTGGCCAAAATTCCTTTAAGACAAATAGTAAATTTCAGCCAGAGCCGCTTCCCCTTGTCTTCTACAAGCACACTGTTGGGTCAATTATAAAAAATCACAATTGGGGTGTGGGGGAGCCCTGGGGGAGATGTAAATAACATCAAGACTTAGTCATTTTAGAGATAAATTTAAATGTAAATAACATCTTGAATTAGTCATTTTAAAGATAAATTTGAAATATTAAAAAAGTTCACACAAGATAATACCATGTTAAATAATACAATTGCAGGAGTGGTCGCCCCACAAGGCCACTCTACGATCTTTCAAGCAGCCTCTCCTTGGCACCTACTGTGTGCAACATACTGTGTTGTGAAATCGTGTTTAGCTCCTGGGCTGCTGCTACCTACGTGGTACAGCAGAGTTGGAAGTGGCCTACAAGTGCATCTCTGCTTTTCAGGTGGACTCTTGAGGCGGGGGGCATGCCATCTTACTCTGGGATTTTCCTACAAATTTCAAATACCTCCTGGATGCGTCTGGGGAAAGGAGGCAACCCGGGCTTCCTGGTTTCCACTCCTCATAGAGGGAGGGAAGGCCTCCAGCCTGGAGATGCTGTGATGGGTGACCCCAGCCGTTTCCTGACTCTCAG
Seq C2 exon
GGTGTCAGTGTGACATCGGTGGAGCCGTCACCCCTGTGTGCAGCGGGCGCTCCGGAGTCTGCCAGTGCCGAGAGCATGTCGTGGGGAAGGCCTGCCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000027181:ENSBTAT00000060991:16
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(64.7=91.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PU(69.6=94.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGATGGTGACTGTCATTGTAAATCCC
R:
CAGGCCTTCCCCACGACAT
Band lengths:
198-960
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]