RnoINT0131124 @ rn6
Intron Retention
Gene
ENSRNOG00000019136 | Scamp2
Description
secretory carrier membrane protein 2 [Source:RGD Symbol;Acc:68348]
Coordinates
chr8:62358645-62360100:+
Coord C1 exon
chr8:62358645-62358762
Coord A exon
chr8:62358763-62359971
Coord C2 exon
chr8:62359972-62360100
Length
1209 bp
Sequences
Splice sites
5' ss Seq
ATGGTAACA
5' ss Score
4.87
3' ss Seq
CCAACCCCTTTTTTACACAGTAA
3' ss Score
5.06
Exon sequences
Seq C1 exon
GCTGTTGCGGCTGCAGCCCAGGCAGGCCTGCTTCGGCAGCAGGAAGAGTTAGACAGGAAAGCTGCTGAGCTGGAACGCAAGGAGCGAGAGTTGCAGAACACTGCGGCGAATTTGCATG
Seq A exon
GTAACAGACTGTCGGGGTCTAGCCTGCTCTACCTGGCACAAGGGGTACTCTTAATCACCTTCATGGGGGATCTTGCAATGCTTTTGATTTTAGAAGCATGTTGGTTTGGGGAGCTCAGCCTAGTGACAATATGTGTAACCCCAGCACACTGGGGCAGAGGCAGAAGGATTACTCCACATTCCAGGCCAGCCACAGCTATAATATAGTATGACTACATCTGGGGAAAAAAAGGAAGGAAGGAAGGTTGCTGATTCTGGGGTAGAAAAAAGTAAGGCAGAAGTTAAAAGATCAGCAGAGTGGGCCTGACAGATATGAGTTATTTCTGCATTCCTTTCCAGCTCTGAAATTCTTCACATGTTGTTGCTAAAACTCCTTCCCAGAAGGAGACATAAACAAGGTCCCAGTGACAAACTGAGGTACAATTCCACCAAAGTTGACTCTGTAGAACCAATGAATTTACTGTTCCTTACAGAGCATGGGTGAGAGGTTACCTACAGGAGGGTGGGTGCTCCTCTCCTGACAGACAGGCTGTCCCTGGAAAGTCTTATCCAGCAGGGACTTCCCTATAGTGGCATACATGGAGCCTTCTTCCCTATATAGTCTGGCCTCTCCCCACGGCCATGTACAATTAAGGCAGAAGTGCATAGAACTTATGGTAGGGAGTGGCTTAGATGAGAGTCTCCTGCTCCACCCCACAAGTCAGCTGGGACAATACTTTTGCAAGAGGGTGCAGTTAAACTTCCCAAGATGGCGGTTGCTTGACTTTTACATGCTTATGATGACAACTTTGGTTGTCCTGCTTATGAGCTAGTCATTAAAAAAAATACTTCTTTAAGCCAGTGTGCTAGCTCACACCTTTAATCCCAGCACTCAAGAGGCAGAAGCAGGTAGATCTCCGTGAGTTCAAGGCCAGCCTGGTCTACATTCAAGGATAGCCAGGGATACCTCACAGTCTTAAAAGGAACAAACACATCATTTGGGACAGTTAGTCCCTCTATTACCTAGGATAGTTGGGCTTCATTATCTTGGAGCAAACTTGTGGGTATCTCTCTGGGTTCCTCTTGATCTCATTTTGTGTTCCTTGAAGCCCCCTGAAACTTCTGAACTCTACTTGTAGGGGCCACCTCCACAAGCTCTGTTTTGCCTATAAACTGGGTGGGTGGTGCTTTCATCTGTGCTGCTGCTGAGGCCAACCCCTTTTTTACACAG
Seq C2 exon
TAAGAGAAAACAACTGGCCGCCACTCCCCTCATGGTGCCCTGTGAAACCCTGCTTCTATCAGGACTTCTCCACGGAGATCCCTGCCGACTACCAGCGGATATGCAAGATGCTTTACTATCTGTGGATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019136:ENSRNOT00000066923:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.383 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF120723=DUF3552=FE(84.8=100)
A:
NA
C2:
PF120723=DUF3552=PD(10.9=11.4),PF041448=SCAMP=PU(42.4=95.5)
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:
TCGGCAGCAGGAAGAGTTAGA
R:
CATCCACAGATAGTAAAGCATCTTGC
Band lengths:
214-1423
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]