DreINT0088217 @ danRer10
Intron Retention
Gene
ENSDARG00000036279 | lamc1
Description
laminin, gamma 1 [Source:ZFIN;Acc:ZDB-GENE-021226-3]
Coordinates
chr2:35986224-35988142:+
Coord C1 exon
chr2:35986224-35986469
Coord A exon
chr2:35986470-35987988
Coord C2 exon
chr2:35987989-35988142
Length
1519 bp
Sequences
Splice sites
5' ss Seq
AACGTGAGT
5' ss Score
9.54
3' ss Seq
TATTTGTCATCTGTCTGCAGCGT
3' ss Score
8.41
Exon sequences
Seq C1 exon
GTAAGCGATGTGAGCTGTGTGACGATGGTTTCTTTGGAGATCCTCTGGGTGAGAAAGGTCCAGTGAGAGCGTGTCGAGCCTGCAGCTGCAACAACAACATCGACCCGAACGCTGTGGGCAACTGTAACCGAGAGTCGGGCGAATGCCTCAAGTGCATCTACAACACCGCTGGCGTCTTTTGCGACCGCTGCAAGCAGGGCTTCTACGGTGATGCCCGCGCTGCTAATGTAGCCGACAAATGCAAAC
Seq A exon
GTGAGTGAAAGGAGAACGAAATATCTGTACTTGGTTTTTTGTTGTTGATTTGTTTTTGATATTTTTCTGGACACTTTTTCAAGTAACAATTGTTTCATATATTTATGTTACAGTTAACTTTAATAACCTGATATTATAGTTGTAAAATGTAATTGGTTTTGGGTAACACTTTAAAATAATAGTCCATTAGTTAATGTTGGTTAATGTATTTGCTATGCATGAACAAAATATTAGTAATACACAATTTATTTATCTTAGTAACGTCAATTATTGTCATTTAAGTTAAACTTATGTTAGTTCATATTAACTTGTGGTGCATTAACTTATGTGAACAAGCACAACTTTGTATTTTAACAATGCATTAGTTAATGTTGAACTATTTTTAATACATTTTTTACAAGATTACTCATTCTTTGTTAATGTTACTACGTTAACATGTATGCTATCCTGAATGTAAGTGTTACCCAATTTTGTTACTTGAATTAATGAAAGATGACCAAAAACACACATATGTAAATAAAAATAACAGCTTAAATAAATGAACATAAATAAATAAAAAACAAACAGCTTAATCAAAGAACAGCTTCTAATTAAATTTGTTTGTAACATTATAAATGTCCACATTTTTATTTATTTAGTACATCCTTGTATTAAAATAATAAATTAACCTCAGATTTGTTTGTATGCAATTGAAGTCAGAATTATTTGCCCCCGTTTCATTTTTTCCCCAATTTCTGTTTAATGAAGAGAATATTTTTCCAACACATTTCTTAACATAAATGTTTTAATAAATCATTTTTCATAACTAATTTATTTTATCTTTGCCATGATGACAGTAAATAATATTTTACTAGATATTTTTTTAAGATACTTCTATACATCTTAAAGGCAGGTTTGGGTAATTAGACAAGTTTTTGTATATTGATAGTTTGTTCTGTAGACTATCTGAAAAAAAATAGCTTAAAGGGGCTAATAATTTAGTCCCTAAAATGTTTTTTTTTTTTTTTTAATTTAAAACTGCTTTTATTCTAGCCGAAATAAAACGAATAAGACTTTCTCCAGAAAAATTCTTTTTTAAAAATAAATATTAAAATTCAAAGGGGGGCCAAAAATTCTGACTTCAACTGTACATTTCAGCTATAAATTGCTTTGTTTGTGTGCATGTGTGAAATGCAAGTTGCAAGTTTATTGTATAATATTAATAACAAATTGGTCGGAACAGAGAAAAATGACATTTGCAGTGATGCATTAGATTTCTATTTCATATACATGCTCTTCTTTTACAATTTCGTTTTATCGTAGAATCACTTAAAAAGAAATAGGTTGAACTAGTTTTTTCAACAACTTGAATAGGAATGATTTTCAGCATTAAGTATATTATGTGATAGAGGTAAAAATAGTTAGTTTGCGGTCAGTTTTTTTAGCTGCATTTATTTCAGAATATATATATTCTAAATAATATTGTGAAATGATTATTTTTTAATGGTTATTTTAAAATGTATTTGTCATCTGTCTGCAG
Seq C2 exon
CGTGCAAGTGTTCTCCATATGGTACAGTAGACCGACAGACAGCCTGTTCTCAGGTGACGGGTCAATGTCCGTGTCTCCCTCACGTCATTAACAGAGACTGTGGCGCTTGTGAACTGGGTTTCTACAATCTGCAGAGTGGAAAGGGCTGTGAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036279:ENSDART00000004277:14
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(45.3=28.9),PF0005319=Laminin_EGF=WD(100=65.1)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=94.2)
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:
CCTCTGGGTGAGAAAGGTCCA
R:
GCCCTTTCCACTCTGCAGATT
Band lengths:
351-1870
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]