RnoINT0131867 @ rn6
Intron Retention
Gene
ENSRNOG00000018657 | Scrn3
Description
secernin 3 [Source:RGD Symbol;Acc:1305064]
Coordinates
chr3:60026746-60028898:+
Coord C1 exon
chr3:60026746-60026906
Coord A exon
chr3:60026907-60028716
Coord C2 exon
chr3:60028717-60028898
Length
1810 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TATGACTTTTCTTTTTACAGTGT
3' ss Score
9.68
Exon sequences
Seq C1 exon
AAATGCAGCCCTATTCCTGTGACACGTTTGTGGCATTACCTCCAGCAACAGTTGGAAATAGGGTTATTTTTGGAAAAAATTCAGACAGACTCTTTGATGAAGTACAAGAAGTAATTTACTTTCCAGCTGCAGTTCATAGTGATCTGGAAAAACGTCTCAAG
Seq A exon
GTAGGTGAAATACATGTTGTGCTAGCAATTATCTATTGCTTAAAATATTCAGGGACAGTTTTATTGTCTATGTATGCTTGTGCACCACATGTGTGTGCCTGGTGCCCAAGGACGCCAGGACAGGGTGTTGGATCTTCTGGAAGGACAGTTACAGACAGTGGTGAGCTGTCATGTGGGTGCTAGGAATGAGCCCTGGTCCTGTACAAGAGCAACAAGTGTTCGTAACCACTGAGAATTTTCTCCAGCCCCATAAATGGTTATTTCTTTCATTAGCTACCAATTGACAGAAGACCACTGAAGTTAAAATTCAAGAATTTAAGGTTGAAAATGGTTTGAATAAAAAATGGACTTCTGGTCTTTTATTTCAACAATTTAGAGGAAGCTGCTAAAATAATAAAACTTGTCTCTTTGATCAAGTATTTGAATACTTTCTACATGTTAGATATGATAAGGAGTTTTCAAATAAGTTATTAAAACCTGGGCAACATCATACCGAAGCTAAGAATATACAAATGGATGCAACTAACCTCAGGATAACATAGGGTGGTTTAAATGCTGGACTTAGGAGTAGTGGCTGGGGCAGCGGAGAAGGAACATCTAGTCAGATTAAAGAGTGGGGATGGAGAGTTGGCTCTGTGGTTAAAAGCACTTGTGGCTCTTTCAGAGGACCCAGGTTTGAGTCTCAGCACATCTATATGGTGGTGGTTCACTACCATCCGTAACTCCAGTTGCATGAGATCCAATGCTCGCTTCTGTCTTCTGCACATATATGCACAGAAATACGTGCATATAAACTACTCATAAAGTAAATAAATAAATATCTCAAAAGTTAGGTAGAGCTGGGGTTTCCGTTGACAGATCAAAAGGATTCTTCTTGAAATAGATTAGAAAAATTATTCCAGATGTTATTAATAACAGGTTTTTGTTTCTTTTTCTATAGTGCTGGGGGAATCAAACTTACGGCCTCCTGTATGTTAGGCACACATTCTAGCAACTGAGCTACATTTTCAGGCCCACAGATAAGTTTTACAGCTCACCCAAAAGGTTTATTAGGGACCTAATACATACATCTTATATGTTTTCCTCACCTCTTATATGCACATTAAATCAAATGTCCTCTAACATTTTTATTTAAAGTCTATTTACATGGAACTTAAAGGTTACATTATGTTCCATTGTTAGGAACTTTTTGGATTCTTGATGTTCTAACACTGATATACATATACGTATAAAAATATAAGACCTTTTGTGTTCTATATCTGTATGTTTAAATCTAGCCCGTCATGATGTCTCCGAGGTCACTGACACCAGAAATGTGGGCCCCCAGCCATTCTCATCTGACTGAAGGTCTCACGAACCTATAATGCATAATGTCACCAGTCAGGACATGCTAGACATTGAACTTGAGGACTGCTTTCTTGCTCTTCAACTCATATTAATCATTCTCCCTGAAACAATTTGAAGATTAGTAACCATCACTCCTAAGCTTCCAAAGCAGCTCTGTTCATCTTCATTTGGGCCTTACTATTTAATATTTTCTGTATCTTAGTTAATGGGGAAGTCTTTGTTTTTTGAATGAAGATCCGTCTTGATTCGTAACTGACCTGTCTTAGCAGGGTATAATAGGACACACTCAGAAAGTAGTTAAATGATAAGTGCTTTAGAGTCAACTCTGCATGAGTTTATTATTGAAAACTTCAATGTAGCTCCATTCCCTACCGCCACTGTGATCGTTCCTTCCAACGGTGTTTTCAGTCCTGGGATTTGGCACCGTTTCATTTTTGGTTGTATATGACTTTTCTTTTTACAG
Seq C2 exon
TGTACTTATATAGAAGTCGATCAGGTTCCTGAAACATATGCTGTTGTTCTTAGTCGCCCAGCTTGGCTGTGGGGGGCAGAAATGGGTGCCAATGAGCATGGAGTCTGCATTGGGAATGAGGCTATCTGGGGAAGAGAAGATATTTCTAAGGAGGAGGCACTTCTGGGCATGGACCTTGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018657:ENSRNOT00000025255:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0357710=Peptidase_C69=PU(12.9=60.4)
A:
NA
C2:
PF0357710=Peptidase_C69=FE(24.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGCAGCCCTATTCCTGTGAC
R:
CTGACAAGGTCCATGCCCAGA
Band lengths:
342-2152
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]