DreINT0088070 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9667225-9669027:-
Coord C1 exon
chr23:9668914-9669027
Coord A exon
chr23:9667411-9668913
Coord C2 exon
chr23:9667225-9667410
Length
1503 bp
Sequences
Splice sites
5' ss Seq
GAGGTTTGA
5' ss Score
3.11
3' ss Seq
ATCTGTTTACTTTGATACAGACG
3' ss Score
6.05
Exon sequences
Seq C1 exon
GTCTAAAGCCACGTGTGGACACCATAAAGATGAGTTTACTTGATGCTGAAAAGAAGAAAGAAAAGATGCTTCAAGACCTGAAGGATATTCAGAATAAACTCAACGTCAGCCGAG
Seq A exon
GTTTGAGGAGCCTTAATTTTTTCAGTCGTTTGTGACTAAGGGCGTACTCACACTATGTACAGTTGCCTTGAACTGGGCCGAAGCACGTTTGTCCCCCCTCCCATCTCCCCTGATGGCCATCAGTGATGCACTGTTCAGTAGAGAAGCGCTCTTGCTCAGCACAGTGGAGATATCTTTAGTTATATCGTTCAGTCGTTTAGGATGCAGTGACACACAGTCAAATATTTCGCCGGATAGAGATCAGCCATTTTGACGCTTATAAACAATCATAAAGTCCTCGTGCTGCAGGAATTAGAAGGTTTGCTGAAGGTGCAGCTGTCGCGCAGTGAGGGGTTTGCATCTTTAATAATCTATGACAGTTTACGTTCATTGAATAGTAAGAATGATTAATATATCCATCATAAAATAAAAAATAATATATCCAATATATCCGCCTCGTCTTCCGTTTCGGGTTCAGGCGCGCTTTGCACTCACACTACAAGCAAAGTGATCGCGCTCTGGCACACCTCTTCCAACCGGGCCAGGGCCGGCCAAGTGACATGTCACAGGGCCGGCCAAGTCACACTTCTCACACGTTTCGGGAAACAGGCCTGGGCATGGATCGGATAGCATAGTGTGAGTACACCCTTAACTAATAGTAAAATAACTTGTAAATAAATCTGTTTTTTAGATGTTTGGGGTTTTAAAGAACCCTAGAAAAAATGCATACAATTGGTTTAAAAATTTTCATTTCAATGAATAAAAAGTATTTTCCCTTTAAAAAGAGCTCACTGAACCCAAACCTTTGAATGCGAGTGAAAGTTAAAAAAAAATTGTTATCCTATCTGTGAAATTTTTATTATTTTTCAAATATTTCCCAAATGCAGCTTAAAGGAGAGAAGTTTTATTCAAAAACGTTTTTTAACATAATAGTTTAATAACTAATTTCTAATGGCTTAATTATTTTGTCTTTCAAATGATGACTGTATATATTTTACTAGTTATTTTGCTATTTTTGTTGTATTTTCATTATTAAAAAAATATTTTAAAGCATATTTTTAATATAATATTTGTAAAACAAATATTTTGAGATTTCAAAAGAAAACACATATAGAACTTACATAATCTCTCATACAGAAAGATACGTACAGATCTTGCATATGCTTTGTATTTTCTTCTCTTTAACAACAAGTATAATCCGTATAACATGGGGAGCTACAAAACCTTTAGAAGATTTCTTTAAAGAAGAATATATAGATGTTTAGACGCATAATATTACATCTAAAAAATACAATTGAAGAAAAATTCGGGCATATTGGTGAAATAAACTCAATCTATTATCTCTGCACTGTATCAATCCATTCCTCAACTGTAGGTGACTCTAATTTTAACCTTTTTTTTTTGTAATTACTTTTTTACTAGCTGCCAGAAGAATAAAAAACAGTTTCTTGTCTTTATTAATCTATCTAAATTATGTTACCTAAATGTAAAGATTCTAAACATTATCTGTTTACTTTGATACAG
Seq C2 exon
ACGACATAGTGAACAGCATCTCAGCAGCTAAGAGTGCGGTGGAGCAGGCTAACAACACGGTGGCTAACGTTAGCGGTGTGCTGGCTCCAATTCAGAAGCAGCTGGAGGAATGGCAGAAGCAGTACGGAGACTCCAACGCCACTAGTGAGGATATCAACAAAGCCCTCAATGACGCCAACACATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:58
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.205 A=NA C2=0.302
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF060097=Laminin_II=PU(40.5=84.1)
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:
CACGTGTGGACACCATAAAGA
R:
ATGTGTTGGCGTCATTGAGGG
Band lengths:
288-1791
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]