RnoINT0132287 @ rn6
Intron Retention
Gene
ENSRNOG00000019122 | Sec16a
Description
SEC16 homolog A, endoplasmic reticulum export factor [Source:RGD Symbol;Acc:2322350]
Coordinates
chr3:3870594-3871279:-
Coord C1 exon
chr3:3871139-3871279
Coord A exon
chr3:3870708-3871138
Coord C2 exon
chr3:3870594-3870707
Length
431 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CTCTGTTCTCTGGGGTCTAGATG
3' ss Score
6.55
Exon sequences
Seq C1 exon
GTGTTTAAATTCATCTACTTGTGCCGCCTGGCTGAAATGGGACTCGCTACACAGGCCTTCCACTACTGTGAAGTAATAGCCAAGAGTGTCCTGACACAGCCTACTGCATACTCCCCAGTGCTGATTAGCCAGTTGATTCAG
Seq A exon
GTAGGAGCTTCCAGGGCCTTCCTGTTACCGTCTCGACAACTCTGGAAAGGCACAGACTTCATCTTGCTGGTCTTGGGGGTGATGGGTGGTTCTTAACAAAGAGAGATCCAGAATTTAGATACTTTAGATACTTTGGTGCTCTTGGGTGGCTGTTTTGGACTTTGCATCATTAACAGTCACTGCTTAACAAATTCATCTTGATCCATTCAAATCCTTTAAGGCTCTCAGAGGACTGCATCTTCCCTGGTTAGTTGAGCACTTAGACAGGCCAGTTAGTATCCATCTAAGTGTGAACTGCACCCGGAGCACTCTGACCACTCAGCTTGGCACAACCCACACGCGGCCTTCTTCAGGCCCACTGTGTTGCACTTGGGAACAGTTTTGTTGGTGCCATTTGGCAATAACAAGGACCTCTGTTCTCTGGGGTCTAG
Seq C2 exon
ATGGCTTCCCAGTTACGCCTCTTCGATCCTCAACTGAAGGAGAAGCCAGAGGAGGAGTCCTTTGTGGAGCCTGCCTGGTTGGTGCAGCTGCAGCACGTGGAGAGGCAGATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019122:ENSRNOT00000064083:17
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=0.026
Domain overlap (PFAM):
C1:
PF129312=Sec16_C=FE(17.4=100)
A:
NA
C2:
PF129312=Sec16_C=PD(12.5=86.8)
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:
TGTTTAAATTCATCTACTTGTGCCGC
R:
CTGGATCTGCCTCTCCACGT
Band lengths:
254-685
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]