DreINT0087977 @ danRer10
Intron Retention
Gene
ENSDARG00000071462 | lama3
Description
laminin, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-050208-475]
Coordinates
chr22:16369568-16371028:-
Coord C1 exon
chr22:16370867-16371028
Coord A exon
chr22:16369765-16370866
Coord C2 exon
chr22:16369568-16369764
Length
1102 bp
Sequences
Splice sites
5' ss Seq
TATGTGGGT
5' ss Score
-0.5
3' ss Seq
GAAACTTGTTTCTCTTACAGTGC
3' ss Score
8.36
Exon sequences
Seq C1 exon
AGTTCTTGGATAAGCTGAATCGGTCAAACAACACAGGTGGAAACACAGAGGATGCAACCAGGATGTTAAAAGAAGCCCAGAGGATGCTGGAGAAGATGCGAAGACAGACCTGTAGGGTTCAGAGAGAGCTGGTCAATGAGGAGTTGAGAAAAGCACACATAT
Seq A exon
GTGGGTGAACTGCTTCCAAATTGCACTTGACCTATGTAAGGTGTATTTATGTAGTGCATTTATTGTGGATGACCATACACCCAGCATTTTACAATCATGAGGGGGGTCTCTCCATACCCCCACCAGTGTGGTGCTATGGAAAATATAGAAAAAATATAGAAAAAATGATAGAGCCAATTCGGTGGATGGGGATGATTGGGAGGCCATGATCTGTAAGGGCTGATAGTGGGAATTTGGCTGAACACTGGGGTTACACCCCTACGTTTTACGAGAAGTGCCATCTCATGCAACATCTCATCCGAAAGATGGCGCTCACTGAGAGTGTAGTGTCCCCTTCACTATACTGGGGCATTTGGACTCACTCAGACCACAGGTTGAGTGGCCCCTGCTGGCCTCAGTAACAACATTTCCAACTGCAACCTAGTTTTTCCATGTGGTCTCCCATCCAGGTACTGACCAGGCTCAGCCCAGCAGGGTTACATGACTGTGACCTACTTCTTGTGGGCCAAGAGCTTGCAGGAAACAGTCAAACATTCCCCAATTTGCCTATTTTAAGTGATCTGTAAGACATTGATTAGCTGGTTCAGTTGTTTAAATGAATTTGGAGCTAAATTATTCAGGATAGTTGCCCTCCAGAAGATAAACCTGCTTTAGTATTTTGTTTTAGGTTCCTTAAAGCCGATTTATACTTTTGCATTGAGTGCACATGGTAAGTCTTTTGTACAGTCACATATCTTCACCATACCCTAACGTGCACCATTTAAAAAAATGCAATTACACATTGATTTGACTTGGTGCACAAGATCTTTAATTGGTCAGCCAAGAAGTGTTGCCAATTGTGGGCGGGGCGAGAGCCGTGGGGATGGACTATGATGGTAAGAGCATTTAACAAATGTTGAGTCCCATGGACAAGCTCCAGATAGATATGTTTTGGAATCACTTAATAATTAATTGATTGATTATTGGTTTGTGCAGCTTTATTCCTTGAATGAGTGTGAGTTTAAGCTACTTCTACAGTATTGGTCACTCGATGCAGAAGTGTAAATCAGGCTTTATTTATCACTAAGCTCCTTTATGGTTTTGAAACTTGTTTCTCTTACAG
Seq C2 exon
TGCTCAGCCTCATTTTGAAAGACCTGATTTTTCCTTTGAATGGTTCTTTGATTGCGGCTGATCGTATTCGTCAGGATCTCATGGATCGGGCAGAAGATCTTCGAGATATACAAGAGGCAATAATAGATGCCCAACTTGATGTGCTCAAGGCCAATGGAGTGAACAAACTCAATGAGGAACAGCTGAAAAACATTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000071462:ENSDART00000135987:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.364 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF060089=Laminin_I=FE(20.6=100),PF138741=Nup54=PD(19.8=41.8)
A:
NA
C2:
PF060089=Laminin_I=FE(24.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGATAAGCTGAATCGGTCAAACA
R:
TCAGCTGTTCCTCATTGAGTTTGT
Band lengths:
342-1444
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]