DreINT0131164 @ danRer10
Intron Retention
Gene
ENSDARG00000040274 | scamp5b
Description
secretory carrier membrane protein 5b [Source:ZFIN;Acc:ZDB-GENE-120215-76]
Coordinates
chr18:50098727-50099089:+
Coord C1 exon
chr18:50098727-50098828
Coord A exon
chr18:50098829-50098971
Coord C2 exon
chr18:50098972-50099089
Length
143 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
TGTTCTCCGTCCTGTTCTAGTGG
3' ss Score
9.55
Exon sequences
Seq C1 exon
GACTGACAGCTCGTTCTACTTCATGGCGTTCTTCTTTGTCTTCATGGCACAACTTTTCATCGCTATCATTCAGGCCATCGGTATTCCAGGATGGGGTGTTTG
Seq A exon
GTAAGAGACTTCAAGCGCAACTGCATACACATAATAGGCATGAATACAATGCAGCATTCTGTATCCTAACACACAGCCCTGCCTGTTGATGCTGGAGTATTGCATGTAGTTTGCATGTTGCTCTGTTCTCCGTCCTGTTCTAG
Seq C2 exon
TGGCTGGTTGGGCACCATCTCCTTCTTCGGCACCAGTATCTTTGCTTCCATCATCATGTTGATCCCTACACTCATGTTCACCGCCGTCTCCGTCATCTCCTTCCTTGCACTAACGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000040274:ENSDART00000058936:5
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:
PF041448=SCAMP=FE(19.3=100)
A:
NA
C2:
PF041448=SCAMP=FE(22.2=100)
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:
GACTGACAGCTCGTTCTACTTCA
R:
TCGTTAGTGCAAGGAAGGAGA
Band lengths:
218-361
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]