DreINT0088095 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9742285-9744468:-
Coord C1 exon
chr23:9744378-9744468
Coord A exon
chr23:9742420-9744377
Coord C2 exon
chr23:9742285-9742419
Length
1958 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
TTCTCTCATGTTTCTTGCAGAAT
3' ss Score
10.66
Exon sequences
Seq C1 exon
CATCACACCACAGGCGTCAACTGTGAGCGCTGTATTCCTGGCTACTACAGATCACCTGACCATCCTCTAGAGTCACCATTCGCCTGTTCAA
Seq A exon
GTGAGTCATACACGTCATTTAACAAATGCTTTTTTATTTAGTTCAGTTCATCTTTATTTCTATAGCGCTTTTACTATGTAGATTGTGTCAAAGCAGCCTAACATAATTTTTTATCCAATAAAAAAAAGGAGAAAGAAGCGATCAAGCCAACAAAAGAGCTACAGTATGTCAAAGTTAATTAGTCTGGTTTTAATTGATAAAAAAATAAATAAAATAGAAATGTATAATGTAAAAATCTTGACACTAATCACTAATCTTGACTAAGGGTCATGTGGCACATCTGCAGCTTGTATTTAGATTTTAATTTGTGCTGTTCCAGAAAAATATATAATAATGATTATTAAAAATATTTGTGAATTATGGTAAGTTGAAAAAATGTGAAAAATGTAAAATATGTTGTAACCTTAAAAACAAAACATTCAGAATATGAAAAAGACATGATTGTTTTTATTAGGACTTGTTAGTTTTACCACATATATTGTGATTAATATTAGTTAGGATTTGCTGAAATAAATTTAAACATGGATTTTTATTAATATTTGCATAGAAAGCTCCAGAAAATGTTTTTGTAAACATTCATTCTTTTATTCATAAATTTTCTTTAACTAAATTGTCCATAGTGAACGAGTTTGTTTGTGTGGAAGTTTCCCAGAGATGGGTTGCAGCTTAAAGGGCATCCGCTGTGTATAAACGTGCTGGATAAGTTGGCGGTTCATTCCGCTGTGGCGACCCCTGATTAATAAAGGGACTAATGCCGAGTTCAGACTGCATGGTTTTCAAAGTAGTCGTGTCACAGATGTTTTCACACTGCATGACTATCTGGGCTAGCGTTTTGTCGCTGCTTTGTTTACACTGCAAGATGGATTGGTGACAAGGGCTTTAACATTGCACGACTTTACAATAGGAAGAATCGCTGACAACTTCGTCCAAACTACATCTCCGAGCCAAAAACACGTAGTATATCATTTATTATTAAAAATGAGAAAGAATCCTTTAATGGGTAGAAACTGTACATATTTGCTCACCTGGGTTTGAAGGAAATAAGCAATTTCTCCTCAACTTTCTTTTTTAACTTTCTGTATGAAGCGTCAAACAGACACGAGTGCTTCTGTCAAACTTCCACTAGTTATTCCTTTATTTCTTGGGTCCAAATAAACTGAAAATGAGCGCTTCTCCCCTCTCTGAAACTTCTCCCCCAGCCTGTGGTGTGGTCCTGCTGACCTGTAGCTACACACACGCAAGTGAATGCTGCACTCTTACTGACTGTAGCCAATCTCCGATGTTATTTCCATCAAAACTCATCTCACACGGCATGATTTAAATCGCCGACAACTCCGGATATTTAGCACGCCAAATATCTCACAGGCATCGTTGACTCATCGGCGATTCTCCCAGATCGCGAATTTGATAGTTCATACTGTGTGATTGTCACTCATGTGCTTGAGCGCCGATTTGCCTGTGATTTCAGGCATTTGTCTGTGATTTCTCCAAACCTGTCGGTGAGTCAAAATCGGGGCTAAAATCATGCAGTCTGAACTCGGCAATACTGTGAATACTGTGAAAATTTCCTTGCTCTGTAAAACACCATTTGGGAAATTTTTCAAAAACAAAAACAAAAACAAAGGGGGGCTAATAATTCTGACTTCAACTATATATATTTATTAATTATATTTATTTTTTTATTATATTTATAGTTTAATAAATAATTAGTATTATTTTCTTTTTAGTACTTAAACTTGTCTTATTATTTCACTTAGTTTCCAAGGTACCATTTTTAAACTGTTAGTGTTTATAAGGTAATCATGTTATCGTGTTTATCATGTTTTCCTCGATTATTAACATTTTTAATTGTTTTATTTAGCAGTAATAATGCTGGTCATACAGTCATATAAATGAAAATACAACTGTAGATATCTTCCTTTCTTCACTTTTCTCTGATTCTCTCATGTTTCTTGCAG
Seq C2 exon
AATGCCAGTGTGAATCTGAGTTCACCGAGGGCACATGTGAGGACCGAACTGGACGCTGTTACTGTAAACCCAACTACACTGGCGAGAACTGTGACCAGTGTGCAGAGGGATACGAACACTTCCCTGAATGCTACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:9
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(41.2=90.3)
A:
NA
C2:
PF0005319=Laminin_EGF=PU(95.7=95.7)
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:
CATCACACCACAGGCGTCAAC
R:
AGCATTCAGGGAAGTGTTCGT
Band lengths:
223-2181
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]