RnoINT0131123 @ rn6
Intron Retention
Gene
ENSRNOG00000019136 | Scamp2
Description
secretory carrier membrane protein 2 [Source:RGD Symbol;Acc:68348]
Coordinates
chr8:62356826-62358762:+
Coord C1 exon
chr8:62356826-62356924
Coord A exon
chr8:62356925-62358644
Coord C2 exon
chr8:62358645-62358762
Length
1720 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
CCTGCTTCTGTTCTCTCCAGGCT
3' ss Score
10.9
Exon sequences
Seq C1 exon
ACAAATGCAGCGACAACAGTTCCTGTCACACAACTTCCTGGGCCCTCCCAGCCAGCAGTTCTCCAGCCCTCAGTGGAGCCAGCACAGCCATCGCCCCAG
Seq A exon
GTACTGGTCAGGAGTCCTTTGGCCTCTCCTGTGCAAGTGGAAATCACCCAAGTCCATAGTTGAACCCTTTGGGTTGGGGGCAGGGAAAGGGCCTTAATCCCCAAGGCTTCTTGTAAATTTCTTTGAGGCCACACCATAGCCCCACTCTTCCCATCAAACACCCCCCACCCCACACCCCCGCCCAGAAGTAAACTCTGCTCACCAGGCTGGGACCCCTGGTGTCTTCAGAGAACACCTGTCCTGTCGCATCACTCCAGGTCCTTCTTAGGACTCAGAATCTGTCTATTTTTTTGTCTGTGGTGCTGCAAATGAAGTCAAGGACCTTACAAATGCTCTGTCACCAAGCTACATCTTTTTAAACCTCATTTATTCCCACCTCCTATCCTATTTGCTAGTCCCTTCACTGAGTCTGGTGAACCTTGTCTGCTTGTGCCTAATGCTGACCTCTGTCACCCTCCCCACCCCAGGCTTCTCACTGCCTTGGTGAGCATGGCCCACAGTGGAGTTGTGTATTGCAGCTCCTGCTTAGACAGGCCAGCAAGTTTCTGCCTGCCCGATTCCTGGCAGCGGGTGAGCCCTCAGAGAGGCAGATGCTACTAGGAGGAGATAGTAGTCCCAGGGACAGCTACATGTGCAAGCTTCCGAAGGTAGGCCCAGTGTAGATGAGCAAGATGAGGGTGGGCTGGGCCCCTGGAGCCTGCCCAGGCTGGGTCCTAGAACCCTGTGAGGTGAGACACTCCTTATGTGTGGGGTAACTTTATGTTCAGCTGGGCTGATGGGATGCAGGGACCCTGCCTCTGTTCCACCAACAGCACAAGGAGACGAGGCTAGGACCAGTTCTAATCCCAGTGTCGGAAGTTCACCTCCCAGGGAGGCAAACTTCACTCTTTGGAGAACTGCTTTGCTGAAATGTGTGCCTGTGTATACACACGCCTAGCTGTCATCTTGTGAGATGACCACTCCTGCTCCCCCAGAGAGGACTGTAGTCTCATTCTTCAGGAGGAAGATGGGGCCAAACGGTGACAGCAGCAGTGGCAAAGGCCCTGAGCCCAGTTCTGCTCAGCCTCACCCCAGAGTCCCCCAACGGCCATTGGCAGGCTCTGTTCTTCTGCAGAGGTGATAAAGCTTGGCCTCTGCATGCTGCGAAGGGCTACACATCATAGACTATCCCCAGGGTTGGCCAGACATCATCCAGGTGGGCCTGGGAGGCAGCTCCCCGGGCAGAGTGGGAAGGGAGGCTACTTTGGTGTGGATTGCTGAGGCTCTGGTGCCTGTGGCCTGCCTCACATCCTCCCTCTTTGCTTCCTGCTTGCAGCCTAGCGTTGTTTCCACTTTGCATACACATTTCAGGCTCTTCCCTTAGCTTCAAGTCTCTGGGCTTCTGGCTTCAGCTTGAGCTCCTGTGCTTTTACTAAAGGACACTACACTTCAATGTAGCCTGGACTCCACTATGGGAGACTAGATGAACCATGGGAGATGGGGGAGGAAGTGGAGAGCCCTGGTAAGGACTAAGGGCTCAAAGGTGGTAGAAGGAGAGTGGGTAGTGGGTCACCTAGGCACTCCCATGGGATTCCTTAATGCCCAAGACACTTTACTGGGCAGGATTGCCTCAGACCACCTGCTAGCTCTTCCTGCCTGGGTGAGGTGCCTCTGCTGGCCTCCCTGGGCTCACATGGTCCCTTTCTCATTGCTGGCTGTTCCCTGCTTCTGTTCTCTCCAG
Seq C2 exon
GCTGTTGCGGCTGCAGCCCAGGCAGGCCTGCTTCGGCAGCAGGAAGAGTTAGACAGGAAAGCTGCTGAGCTGGAACGCAAGGAGCGAGAGTTGCAGAACACTGCGGCGAATTTGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019136:ENSRNOT00000066923:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.970 A=NA C2=0.383
Domain overlap (PFAM):
C1:
PF120723=DUF3552=PU(0.1=0.0)
A:
NA
C2:
PF120723=DUF3552=FE(84.8=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:
AATGCAGCGACAACAGTTCCT
R:
CATGCAAATTCGCCGCAGTG
Band lengths:
214-1934
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]