BtaINT0084147 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008817 | LAMA4
Description
Bos taurus laminin, alpha 4 (LAMA4), mRNA. [Source:RefSeq mRNA;Acc:NM_001205965]
Coordinates
chr9:38765148-38767039:+
Coord C1 exon
chr9:38765148-38765264
Coord A exon
chr9:38765265-38766859
Coord C2 exon
chr9:38766860-38767039
Length
1595 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
TCCTTGTGCTCTGTGTGAAGGTG
3' ss Score
7.8
Exon sequences
Seq C1 exon
GCAGTGATGAGGCAGTGGTGGATACCAGCAGGCGCGTGGGAGGAGCCCTAGCAAGGAAGAGTGCTCTCAGAGACAGATTAAATGATGCCATGAAAAGACTGCAGGCCGCAGAGAGAG
Seq A exon
GTGAGGGTCCCAACCAAAACGTAAGCTCTTCTGTTTGTTCACTAATATTAAGGGAAACCTCTGAGGAAAGAGTAGGTGATTCCCTGCTTATTAATCTTTTTATAAATAGTATTGCTTTCTGATGACAAAAGAAACTTCGTTTATCTCTCACACACACACACACACACACACACACACACAAAAGTCCTGAAAGATAATAAAAGCTGTAGCTACATCACCTAGGGATGACAATTAAATTTAAGAGCATTTTCCTCCAGTCTTGTGTGTGTGGGGGTGTGGGTGTGTGTGTATGTGTGTGTGAATGAGATCAGGATGTTTATACTGTTGGGTAACCTACTTGTAAACATTCCTTTTCATTAACAAATAAGCCCCAATTTGGTTATTGGGTTTCTCTGACCCCAGCAATAAACAGCTGCTCTCTGTTACATGGCATGTCTTTCTTATAATGCAAGCAGAGAGACCACCTAGCCAGAGAGGGAAACAAGAGCACTCATGTTGCCTAATCTGAAACTATGGGGGTATCTCAGAAAGATGTGATGGGAAGCAGATGTGCCTTTCCCAGCATAGTGAAAGTTAGCACATTACTGCTGGATGTGGGGTTTCACTACACGGAGCAAATCCGGCAGCAGTACCACCGGACACCAAAGCCCTGGCCAGATGGGTCCATCTGATCGGCGTCATCAGAGCTACTACATGCTAAGCCCTGGGCTGCATTTTACAAACATCATCTCATGTGGGAAAGTATTGCTTTTAGGCTGATGTGAACCCCAAGGCTTGTCAAGTCTGGGGAGCTTGCTCTGAAAGGTACAGCAACACAAAGACGATGACCCAGGATTCAAAGCCACAACCGTCACGAGTTCAGAGCGTGAGAGGTTGAGTTAAATGTTTCTCTGGTTAAAAAAAAAAAAAAAAAAAGAAGAAGAAGAAGCTAAACCTCACCTGAGAGATTGTTAATTGTTTTTATTTACAGAATTAATGCATGCCCATTGTAGAAAAATTAGAAAATATGGATAACAAAAGAGAAAAAACAAGGGAAATCTGTTATAATTTCATTATCTAGGAAACAAACGTTTTGTTGTAAACTTGTTTTTATTTTAAATATATAACTTAAAAATTGCACTATAGATCTCTTTTGAAACTTACTTTTCTTATTCAAAAATACCTTTTCTTACCAATTTATGTCTGTACTAGAGCATCATTTTTATGGCAGAAGGAAAGTGATATTTACAGTGGATTTCAAGCAAACATTTTATGAGTTAGTATCTCATACACATTTTGTATAGTTTTCTCACCAGGTCTCTAACTTGAAGTAATACTACTCTTTAAAAAAAAATTACCTCTAATTTGGAAATGTTTTAAATGAACTACATTATTTTATTGAGACTTTAGAGTCTTTCAATCTCATTTGTCAATACTGTTTACAGTATTCTTATGCACCTAACTTACACCATGATTAACATGCATATAAAGGTCTCAGTTTGACTGAAAAGCCTGAATTTGAGGTCTGTTTCATCCCAGTGATTAAATGAGTATTCATGATCCCATCAAAGGCCCTACTTCTTTGCAAAATAAATGTCCTTGTGCTCTGTGTGAAG
Seq C2 exon
GTGATGCCCAGCAGCGCCTGGGTCAGTCCCAGCTGATCACCGCGGAAGCTAACAAGACCACAATGGAAGTCCAGGAGGCAACCGCCCCGATGGCTAGCAACCTAACCAACTGGTCACAGAATCTCCAAAGTTTTGACTCTTCTGCTTACAACACTGCCGTGGACTCTGCCAGAGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008817:ENSBTAT00000011612:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.600 A=NA C2=0.656
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF060097=Laminin_II=PU(39.8=83.6)
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:
AGTGATGAGGCAGTGGTGGAT
R:
CTGCATCTCTGGCAGAGTCCA
Band lengths:
295-1890
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]