DreINT0088041 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9704105-9705729:-
Coord C1 exon
chr23:9705537-9705729
Coord A exon
chr23:9704232-9705536
Coord C2 exon
chr23:9704105-9704231
Length
1305 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
ATATCTGCTTTATTTCCCAGAAC
3' ss Score
9.43
Exon sequences
Seq C1 exon
TGGCTCCTGCATCCCGTCCCGTTTCCAGAATCCTCCTCAGTCTCTGGTCCTGAAAGAGGGTCAGGCTTCTTCTGTCGCAGAGCCGATTCTGGCTTCAGCCCCTGACCCATCTCTGTATGCCGACCGACCCATGACCTCCACACCGCCGACCGCAACGGATAATACTGAACACGTGCTTCTGGACACTAGTCAG
Seq A exon
GTAAACACTGGGACTCATTTTGATTACAAAATGAAAAAAAAATTAAATAAATAAAATAAAAAAACAATAATAATCATAATAATACAATTAATAATAATAATAATAATAATAATAATAAAATTAATGACAGATACAAAACTATCTACAAAATATATTGTTGTTATTATTATTATTATTGCAGATATGTTATCTGTTTTTGCACTTAAACCTTTTCATGCATTAATACTTGCTTTTTCTAAAAGTCAGTGTTTTACTTCTGTCAAATGAACTATTTCCCACATCTAATTAGTCATGTGTTGTAGTTTGTCCTTCAACTATACACTCACCGGCCACTTTATTAGGTACACTTTACTTGTACTGGGTTGGACTCCCTTTTGCCTTCAGAACTGCCCTAATCCTTCCTGACATAGATTCAACAAGGTACTGGAAGTTTTTTCCTTGGAGATTTTGGTCCATATTAACAGGATAGCATCACACAGTTGCTGCAGATTTGTCAGCTGCACATCCATAATGCGATTCTCCCGTTCCACCACATCCCAAAGGTGCTCTGTTGGATTGAAACCAGTCTGAGATGATTCGCACTTTATGACATGGAGCGTTATCCTGTTGGAAGTAGCCACCAGAATATGGATACACTGTCATAAAGGGATGGACATGGTTAGCAACAATACTCAGGAAGACTGTGGTGTTGACACAATGCCCAATGTGTTCTAATAGGCCCAAAGTGTGCCGCCTGAACCATTAATACAAGGCAGGATGTATCCATGCTTTCATGTTTTTAATGCCAAATTCTGCCCATCCGCCTTAGGATTCGTTGTGATGTGCATTCGGAGATGCTCTTCTGCATACCTCAGTTGTAATAAGTGGTTGTTTGAGTCTCTGTTGCCTGTCTATCAGTTAGAACCTGGCCATTCTCCTCTGACCTCTGGCATCAACAAGGCATTTGCGCCCACAGAACTGCCGCTCACTGGATATTTTCTCTTTTTCGGTCCATTCTCTGTAAACCCTAGAGTGTGTGAAAATCTTAGTTCATTAGCAGATCAGACCACCCCGGTCGGCACCAACAACCATACCATGATCAAAGCCTCTTAATTCAGCTTTCTTCCCCATTCTGATGCTCGGTTTGAACTACAGCAAATCGTCTTGACCATGTCTACATGTCTAAATGCATTGAGTTGCTTCCATATGATTGGCTGATTAGAAATGTGCGCTAACGAGCAGTTGGACAGGTGTACCTAATAAAGTGTATTTGAATGCTAATAAAAAAGCAGGTCTGCAAGTCCTCATATCTGCTTTATTTCCCAG
Seq C2 exon
AACGCTGTGGTGTATTCGACGCGTGTTCATGCTCTGGGACGTTACGTGTTCATCCTGCATTACCATCAGCCCCTGCATCCAACGTACAACGTCCAGGTCTTCATCAACGGAGGTCGCATATGGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.277 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TGGCTCCTGCATCCCGTC
R:
CTGCCATATGCGACCTCCGTT
Band lengths:
319-1624
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]