BtaINT0084166 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008817 | LAMA4
Description
Bos taurus laminin, alpha 4 (LAMA4), mRNA. [Source:RefSeq mRNA;Acc:NM_001205965]
Coordinates
chr9:38801129-38803031:+
Coord C1 exon
chr9:38801129-38801284
Coord A exon
chr9:38801285-38802871
Coord C2 exon
chr9:38802872-38803031
Length
1587 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
GAAATGCCTTCTCCTCTCAGATA
3' ss Score
8.7
Exon sequences
Seq C1 exon
GTGATATTTATTCGGGAAAAGAGCAGCGGCCGAATGATAATTGATGGGCTTCGAGTCTTAGAAGAAAGTCTTCCCCCTACAGGAGCTGACTGGAAAATCAGGGGTCCTATTTATTTGGGAGGTGTGGCTCCTGGAAGGGCTGTGAAAAATGTCCAG
Seq A exon
GTAAGCCAGGTGTGATCAGGTAGAGCCATCCACCTTTAGAGTTGAAAGATTGTTTAATGTAGCCCTCGCTTCACGATTAGAAAACTGGCAAAAGTAAAACTGTACTTTGGCTGGAGACGGGATACATAAGTGGGTATTGTTTTATGGTTGTCTGTCCACCCTGTGACATCACAAAGCCTGGAGTAACCTTTTGATTCTAAGGTAGAGGTGAGATGAAAAATGTTTCAGAGGTATAAACTGTCATGAAAAGTTATGTCTCAAGGGCATGCTTATTTGTTCAGCAAGTACTCATGCTTTTAGTCTTAAAGAACACCCAAAAGAGAATTCCCTGGTGCTCCAATGGTTAGGACTCAGTGCTTTCACCGCCCAGGCCTGGGTTCAATCCCTGGTCAGGGAACTAAGATCCTGCAGGCTACATGGCACAGCCCCCCCAAAAAAAAATTACCCAAAAAAGAAAGCGAGTCATTATATTATATATTATTGGGTTAAAAAGAAAAACTTTCAGGCCATTATGTAAACTATGATCTCATCTTCATTTCTTACACACACACACACATACACACAATTTGTAATTGTACAAGGAAATGTGGCTACCCCTTGGGGGACATGAGGATATGGTAGAAGAAAACAACATTATTTTTGTAATGTAAAAGTTTAAAATATTGGACCTTCAAAAATATTTAGCAAAAAAAGGAACGCATCAAAGGACTAAGCTTATTTTTAATATAAATACAGGTTTGACTTTAACACAAAGAATACACTTCTAAGATCCATTAAATGGCTTCCCTGGTGGCTCACTGTAAAGAATCTGCCTGCCAATGCAGGAGATTCAGGTTTGATCCCTGGGTCAGAAAGATCCCCTGGAGAAGGAAATGGCAACCCACTCCAGTATTCTTGCCTGGAAAATCCCATGGACAGAGGAGTCTAGCAGGCTACAGACCACAGGGTCGCAAAAAAGTCAGACACAATTTAGTGACTAAACAACAACAACAAAGATCTATTAATATGTGTGTGTAAAGCAAAAATGGGGGGAAATGTTCATATTTAATTTTATTTTAGATGAGTAGCCCCAATTCCATGACAGCTTCTTTAAAAGAAAGATTTCTAAATCTGTGAAATCGGTTATCTAAAGTGGCCTGTGTTTCATGTCCTGTGGTATGATAAATGCTCAAACACAAGCCAATAAAGCAAATTCTCTGCTGTTTATTTAACCATGGTAGATTTAACAGTTTAGTTCTTTGCTAGCCCTTATCAGCATTAGGTGATCTAGGGCACAGCTGTCTTTCTTGAAGAAAACAAATGAGAATATTTCTAATTCAGTTTGAAAACCACAGCTGCAATTTACCTTGTTGTGAAAAATGTTGAAATTTTTGTACCTTAATTACAGTAGGCTATTATTACCTAATACAAAATTCTAGCTTCAAAGATCTAGTTAAAAAGCAACAATCTGGAAAATGATCGATTATTCAGATAGCTAAAACAAATAGGGCAAGAAATTACTAGGTTCCTCTCAGGACACAAATCCCTTCATTGGTGCGTCTGTGAGTGTTGAGAAAATGGATTTTAAGAAATGCCTTCTCCTCTCAG
Seq C2 exon
ATAAACTCAGTCTACAGCTTCAGTGGCTGCCTCAGCAATCTTCAGCTCAATGGGGCCTCCATCACCTCTGCTTCTCAGACATTTAGTGTGACTCCTTGTTTCGAAGGTCCAATGGAAACAGGAACATACTTCTCAACAGAAGGAGGTTACGTGGTCCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008817:ENSBTAT00000011612:33
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:
PF0221019=Laminin_G_2=FE(39.8=100)
A:
NA
C2:
PF0221019=Laminin_G_2=PD(14.1=33.3)
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:
TTTATTCGGGAAAAGAGCAGCG
R:
CTAGGACCACGTAACCTCCTTCT
Band lengths:
310-1897
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]