DreINT0088044 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9701143-9703380:-
Coord C1 exon
chr23:9703265-9703380
Coord A exon
chr23:9701355-9703264
Coord C2 exon
chr23:9701143-9701354
Length
1910 bp
Sequences
Splice sites
5' ss Seq
CAAGTATGT
5' ss Score
7.44
3' ss Seq
TCACGTCTTTCTCTTGTCAGCCC
3' ss Score
7.66
Exon sequences
Seq C1 exon
GACTATGTGCTGGTGGTGCCAGAGGGCAGTTACAGCTCCAGCTTTCTGTCCGAGGAGCTGCTGGATAAATCTTACGATTTCATCAGTAACTGTGGACAAAACAGCTTTTACATCAA
Seq A exon
GTATGTTATTCAGTGTGGGAAATGCACCATAAATATTTGAAATGGTTGTAAATTTATATAGTATAAAGTAAGCTGAATTGTGGATATTCAAATTCTGGTAAAACTTAACAATACATTACTGAAAAAAAAACAGCTTAAACCAGCATATGCTGGTTGGCTGGTTTTAGCTGGTTGACCAGGCTGGTTTTATAGGGGTTACAGCCATTTCCAGGCTGGTTTCCAGCCATTTCCACCCTGGTCTTAGCTGGTCAGGTTGGGAGATGACCAGCTAAAACCAGCTTGACCAGCCTAGCCAGGCTGGGAGCCCAGCCAAAACCAGCTATGTCCACCTTAAACCAGGCTGGTCAAGCATATTTTAGCTGGATTTAGCTGGTCATTTTCCAGCCTGACGATCTAAGACCAGGCTGGAAATAGCTGGAAACCAGCCTGGAATTGGCCAAACCCCCACTAAAACCAGGCTGGTCTACCAACTTAAACCAGCCAACCAGCCTTGGCTGGATTAAGCTGGATTTTTCAGCAGGGTAAGGTTGTGTTAGTTAATGTGTTTAGTAACATGAACAAACAATGAACAAAACATTCATTACAGTATACCTTTATGATAGTTTATGTTAGGTAATGAAAATAAAGTCATTTATTGTTAGTTCGTTAACTTGCAGTGCATTAACTAATGTTAACAAGCATTAATTTAGATGTCAATATGGTGGTATTAATAAATGCTGTTGAAGTATTGCTCATAATTAGTTCATGCTAGTAAATACTAGTGGTGGGCCGTTATCGGCATTAATGTGCTGCGTCCTGTAATGTCCTGTAATTTTGGGTGACTTTAACTGCAGTTTCACTTTAACTCGTGAACATTTCATTCATATCCCCGTGACAAACTGGGGTATTAAAACAAATAAGGAGTAAGAACTGGTGAGACTGTTATGGAATTTAATAACGCATGCCAAACGGAAAGAAAAAACTTCCGCATTTTCCAGTGTGTGTAAGTGTGTGTGTGCGGTCCTTTACTGACAAGTCGCGTGTGTGGATCTTGTCGGAAAATATTGCTTAAAAGACCTACATGACTGTAATAGTTTGATTGCTGTGTTTATTTCAATAATGCCACTAATATATGCAAACTAATGCATGTATTAATTCCATTTCTGTTTAGTTCAGTTATGACTTTAGTCAGATTAAGGTGATCAAAAATCACTGTTTCAAGCTTATGTAGGCCTACAGTTCAAAATTCATGTTTAACTGAATAAACAGTTAGTAAACGCAAATACATCTTATTGAACATTTATTTTCATCAACAATTATCATAGTAGAACAGCTTCTCAAGCAGTTGCATTTTGGAAACAGGAGATGAGCCCCTGATCTAATGCGCCACCTGGCTTGAGAAACCCGTTCTCAAAGAATTACTTTTAGTCATTATTTAGGTAGCATACATATTCTGAATGCCTTCAGCCGAATTCAAATGAGCCATTTTAATCTAGATTCATTAAAAAAATACTATTAAATGTGTTTAATATAAATTAACATAAATTACATTTTAAATAATACAATAACAAGTTAATTTAGTTTTCGAAATGTTGTCTTTAGGTCATCATTAACCAATCATTTGGTATCATAATGTACACTATGAAAAATAAATATTTATTTTGAACCAAATTTTTACCAAAATTGTAATTAAACTAAAAATGCTACAAATGCCTTTCTTATAACAGTTTTCTCATATATATTTTTTTCAGTTTGATTAATTTATTAAAATGTGAACATACAGGGAAAAAAACAAATAATATGGAAAAACAAATGATACCAATACATGGGGAGAAAAAAAAGAATCTTGTATCAAATATAGTTTGCAAATACCATTCACATGTGTAATATAATACATAATAATACTTAACATCACGTCTTTCTCTTGTCAG
Seq C2 exon
CCCTTCCTCAGCGTCTGCGTTCTGCCTGAGCTCTGCCGTATCTCTGTCTTCCTTCTTCAATAACGGCGCTGTACCCTGCGGCTGTCATGAAGTGGGTGCCGAGAGTGACACCTGCGAGTCTTTCGGTGGACAGTGCAGATGCAGACCCAATGTGATCGGCCGAGACTGTTCCCAGTGTGCCACGGGATACTACGGCTTCCCCAACTGCAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:33
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:
NO
A:
NA
C2:
PF0005319=Laminin_EGF=PU(91.8=62.5)
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:
GACTATGTGCTGGTGGTGCC
R:
GTCTGCAGTTGGGGAAGCC
Band lengths:
328-2238
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]