DreINT0088016 @ danRer10
Intron Retention
Gene
ENSDARG00000020785 | lama4
Description
laminin, alpha 4 [Source:ZFIN;Acc:ZDB-GENE-040724-213]
Coordinates
chr20:240246-241138:+
Coord C1 exon
chr20:240246-240329
Coord A exon
chr20:240330-240986
Coord C2 exon
chr20:240987-241138
Length
657 bp
Sequences
Splice sites
5' ss Seq
TCAGTGAGT
5' ss Score
7.68
3' ss Seq
AACATCATTTGACTTCCCAGGCT
3' ss Score
5.76
Exon sequences
Seq C1 exon
AATGCGACTGTCCAGAAGAGAACTGTGACCTGCACACAGGAGAGTGTCTGCCTGAGCTCTCGCAAATCAGCGAGTGTAATATCA
Seq A exon
GTGAGTTCAGTCACAAAAACAAACCAGGTCAATTAATTCAGCGAGACATACAAAGCAGTTCAAATAATTCCAACATTTTAAGGGGATCCAAAGATGTCCACAACCACAAAATCTGGCGGTTTTGTTTAGAAAATATAATAGATTTACACTCTAAGAAAATGCTGGTTGTTGTAACCCAACACTGGCTCGAATAAAACTCAGCCGTTGCATTAAAAAGTGTCATTTAAATTAAATAGAAAATAAAAGAATTACGCCATGCTTGATTTGCCATATTCAACCAAACGTTGGGTCAACACATTTCTGCACATAATAGTGTGAATAACTCATCTCTAATCACTGATTTATTTCCTCTTCTCCATGATGACAGTAAATAATATTAGACTAGATATTCTTCAAGACACTAGTGTTCAGCTTACAGTGACATGTAAAGGCTTCACTAGGGTAAAGTTAGGGTAATTAGGCAAGTCATTGTATAACAGTGGTTTGTTCTGGAGACAATCCAACACTAATATTGCTGAAGGGGCCAATAATATTGACCTTAAAATGGCTTTTATTCTAGCCCAAATAAAACAAATCAGACTTTCTCCAGAAGAACAAATATTAGAGGAAACACTGTGAACAACTCCTGAATCTGTTCAACATCATTTGACTTCCCAG
Seq C2 exon
GCTGTGACGCGTGTATCTGGAATCTGATCGGAGACATTCGCCAGTCCAACAAAACTCTGGACCAGGTGAGGAACAGCGTGCTGAACATTTCCACAGGAGCTGCAGCTAATGACAGACTGAAGTACTACAACTACACTGCGCACCAGCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020785:ENSDART00000002661:8
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(2.1=3.4)
A:
NA
C2:
PF060089=Laminin_I=PU(12.1=62.7)
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:
TGCGACTGTCCAGAAGAGAAC
R:
TAGCTGGTGCGCAGTGTAGTT
Band lengths:
231-888
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]