BtaINT0084070 @ bosTau6
Intron Retention
Gene
ENSBTAG00000027181 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:HGNC:6483]
Coordinates
chr24:33247112-33248257:-
Coord C1 exon
chr24:33248120-33248257
Coord A exon
chr24:33247159-33248119
Coord C2 exon
chr24:33247112-33247158
Length
961 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
TATTTATATATCATATCCAGGCT
3' ss Score
4.9
Exon sequences
Seq C1 exon
CCTGCCAGTGTTCAGCCCTTGGGTCCTACCAGACGCCCTGCAGCCCAGTCACTGGACAGTGCGAGTGCCAGCCGGGGATCACGGGACAGCGGTGCGACAGGTGTCTCTCGGGCGCCTCTGATTTCCCCCACTGCCAAG
Seq A exon
GTAGGGAAGACCGCAGATGGCTGGAGGGTGGGCTCCTCTCCACTTTGTGCGTGTGGCCAGCCTCCCAGAGAAGCCTGCAAAGCCTGCCAGACCCACCGCTGGCCACTGCTTCACTTTTAACCCTGATCTGTCTGATTCTTCCCCTTGTAAGGTGAGATTGACTAAGGCAAGAAATTAATTAATTGTAGACATAATTTTAGTACGGGCGGAGAGCAAAGGGGCTGTGATAATGAAGGAAGTAAGTCTTGGTTAACTAAAAAATGTACTTACAAATTCTATAACAGCTAATTGTTAGTGTGTTAGTCACTCAGTTGGGTCCATGACTGTAGCCCACCAGGCTCCTCTGTCCATGGAATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCATGCCCTTCTCCAGGGGATCTTGCCTCAAACTCCAGTCTCCTACATTACAGGCAGATTCTTTACCTTCTGAGCCACCAGGGAAGCCCAGCATCAAATTGGACAATTAAAAAAAAAAAAAAAAACTCTTTGTATAATACTGCCCTCTTCTGGATAATTCTAAGGATATTCAAAATTCTAGACTTGTTTCCCCAGTCTCCTTTTCGTCATTTGGAAATGAACTTTTAGGAGGAGGCAGGGAAGAGAGTCGTTGGGTGACCAAAAGGGTGATTTGGAGAGTAAGGACCATGAAGGCTATTAGAGGTGTCTTTTTCTGAATTACTGAGTTGGTCCAGAAGTTCTTTTGAGTTTTACCATAAGATGTTATAGAAAAACGCAAATAAACTTTTTGGTCAACTGAATACATGCAAAGACCTTGCCACCCATCTATCAAAAAATATAAATATAGATGCACTAGTTTTAAAAACAAGGAAAACTTAAAGAAAAAAAACTTTGAAACATCAAAACAAAGGGACAAATGAACATTAAAACCCCAGACATTTCTATACCATATAACTATTTATATATCATATCCAG
Seq C2 exon
GCTCCAGCAACGTCTGTGACCCAGCCGGAACTGTGGACTCCAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000027181:ENSBTAT00000060991:12
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(0.1=0.0),PF0005319=Laminin_EGF=PU(88.2=95.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(9.8=31.2)
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:
CTGCCAGTGTTCAGCCCTTG
R:
AAACTGGAGTCCACAGTTCCG
Band lengths:
183-1144
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]