BtaINT0084173 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008817 | LAMA4
Description
Bos taurus laminin, alpha 4 (LAMA4), mRNA. [Source:RefSeq mRNA;Acc:NM_001205965]
Coordinates
chr9:38713876-38716309:+
Coord C1 exon
chr9:38713876-38713971
Coord A exon
chr9:38713972-38716157
Coord C2 exon
chr9:38716158-38716309
Length
2186 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAAA
5' ss Score
-1.5
3' ss Seq
ACATGCCATTGTACCACCAGGCT
3' ss Score
6.61
Exon sequences
Seq C1 exon
CGTGCAATTGTGGGGGAGGCCCATGTGACAGCATAACCGGAGAGTGCTTGGAAGAAGGTTTTGAGTCCCCTACAGGCACGGACTGCCCAACCATAA
Seq A exon
GTAAAAATAACCGTACATGATTGACTAACCCCACTTTCTCTAATATGCTGCAGGTGTAGGATTAAGAAGATCTATGCAATCCCACCCTCTCTAGAAACTGAGTCCCACCGTTGGCTTTAACCCTGTCTGTGCCTCAACCAAATGGACCCTAAGCAAAAGACATTCAGTCCACTTGATTCCAATTGGCAAATAGCAGGTTGCATTTAAACAGCTCTATTTTAGAAAAATTATTTTTTTCAAGTCTTTAAGTTCAACATCTTACTTAGTAGGTAAAGTTGGAAATACAGTTCCCAATGACTGAGTTCATTTTAGGTCCTTTTTCTATATTATATCTTCAGATCCTCAGATAATGTAATCCATAGACAATGCTTTACAACATTTGGTAAACTCATATACCAAGAGATTTAACTTTTCCCCAGATCACTCCAAATCTGAAGTGGCACCAGTAATATAATATTCAGTCCTTATGAAAAGGAGCTGCCTTCTCTCTTTCCTGTCTTTCCTGTCATTCAAATCATGAAAGTGAAAGTGAATGTTGCTCAGTCGTGTCCAACTCTTTGGGATCCCGTGGATTATACTGTCCATGGAATTCTCCAGACCAGAATACTGGAGTGGGTAGTCTTTCCCTTCTCCAGGGGATCTTCCCAGCCCAGGGATTGAACCCAGGTCTCCCACATTGCAGGTGGATTCTTTACCACCTGAGCCACAAGGGAAGCCAAGAATACTGGAGAGGGTAGCCTATCCCTTCTCCAGTGGATCTTCGCAACCCAGGAATCGAACCAGGGTCTCCTGCATTGCAGGCGGATTCTTTACCAACTGAGCTATCAGGGAAGCCCACTTCAAATCATGAGTAGTCCTAATGGTCCAAGAACCTGCTGAAACATTTCAAAACAAATGCCCAGAGCCAGTCTTAATGACTTCTCAAGCATCCTTTAAGCCAGTAGCCTAGAAAAGTCCATGATTGATTTTTAGAAGGATTTAAGGAAAGTTTTGCCTTAGAAAGCCTTCTATCAAGAAAGTAACTAATATTTGGCTTTAAGTAGAGTGTTTTAAAGACTACTTTAATATTAGATATCTCTTCCCCCAAACAAAATCATCTTGGCCTCTCAGTCCCTCTGGGCACAAGAGATTAATATCACGATGAACCCCATATTAGAAGGTGACACAGGATGGAAGGCACAGGCTGGGCAAAGTTTGCATACTGACAGCATAGGTGATCCTCTATGCACAGTCACTTTAAGGACATCAAGGTGCCTGCTTGGCCTCTCTGTGTCTCCTCCACCAGCCTGATGTTCTGGCTGGGGAGTCATTACTTAGACAGAGCATATGAGGAAGACCTCATTAAACTTCAAGTAACAAATTAACATATTAACAACCATTAACCCTTTAGTCTCCATGTATCAGTTCTCTAGACGAGAGTATATCTGGTGGAAAGAGGTTGGAAACAGAAAAATTTCAAAGGGTGTCCTTAGTGAGTGTGTCCTAGGAGGGCATTGGTTTGTGGGGGTGATGACAGTGGTCAGAGGAACTCGAACATGAAATGCAGGAAGCAGTGAGAAACCGCCACCCTCCTCACCACACGTGCAGGGTCGTCAGCTGTCAGAGAGTAATATTAGCAAACAGTGAGGTCCTGCCGATCTATTCAGACAGGAGGTCAGGCCATGGAGAGGCACCGGGCCATCCGTGCAGTGAGGAGAAAGCACTGGAACCTGAACAGTCAGTAAGGAAAGCTGCTGGGAAAGGAGGAATGGCAGGCGAGTTCCATCTTCACTGGCCGGCACCAAGCGGAAACCCACAGCCTGACGTGGAGGGCGTCCTCCCAGACGGCTTTCCCCTGACCAGAGAAAAGTGGGGAGAAGGTTCTTTTCAGCCACCCGCCGTCTCTCAGATGCCTTGCCCTTTGCGCTTCCTTTCCTCCTCAGCTCAGCCATTAGCGTTCATGGTAACCTGCTTTTCAGTTGCATGTTTGTTTTTTGTGTTTTAAGCAGGGATAGTGCCCAACGTACACTTTGGTCATCTGAGGCTCTCTGAGTATAAGGACTAGTTCCGTGGTCCAGAATATCTCCTCAGGAAACAAAAATACGAACAGTATTAACCAAGCAAGGGCATATAATGACCAACTTAGAGCAGAATGCTTCCCAGCTGACCTTTGATTTTGAGGAAATGACATGCCATTGTACCACCAG
Seq C2 exon
GCTGCGATAAATGCATCTGGGATCTGACTGATGACCTTCGGTTAGCAGCGCTCTCAATTGAAGAAAGCAAATCCGGCCTGCTGAGTGTGTCATCTGGTGCCGCAGCTCATAGGCACGTGAACGAAATCAACTCCACCATCTACCTCCTCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008817:ENSBTAT00000011612:6
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:
PF0005319=Laminin_EGF=PD(1.8=3.0)
A:
NA
C2:
PF060089=Laminin_I=PU(11.0=56.9)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]