RnoINT0132292 @ rn6
Intron Retention
Gene
ENSRNOG00000019122 | Sec16a
Description
SEC16 homolog A, endoplasmic reticulum export factor [Source:RGD Symbol;Acc:2322350]
Coordinates
chr3:3866496-3868173:-
Coord C1 exon
chr3:3868091-3868173
Coord A exon
chr3:3866646-3868090
Coord C2 exon
chr3:3866496-3866645
Length
1445 bp
Sequences
Splice sites
5' ss Seq
CTGGTACTT
5' ss Score
4.74
3' ss Seq
TTCATCTTGCTTTGTGACAGGGC
3' ss Score
8.27
Exon sequences
Seq C1 exon
AAATGGTGCCACAGGGCTCACCTGTCAGACACTCCCCTCCTGAGCCCCGTGAAGAGGAGTTTGGCAAGAACGTCGCTGACCTG
Seq A exon
GTACTTCTATAGCTTGTTGTTGTGTCCCCTGTGAGTTTATTGAGTAGGCACTTTGGCTCCTTGTTCTTAGCCTGAAATAGGAAGGTAAGGAAGGTAAGGAAATTGTTCTTAAATTCGATTCTTACAGAGGAAGTGTTTCTAAGATCATTGGAGCTGAGGCCAGGGAGATGGGTCATTTGTTAAGGGTGCTTGCCACCAAGTCTGATGACCTGAGCTCATTCTCATATGGGAGACAGAGAGAACCAACTCCTACAAGTTACCCTCTGACTTCCACACATGTATTCTAACACACATGCCCTCCAGGACACATTAATTTAAAAGTAACTTTAATTATTCAAATGTTGGTAAAAATGTTGATGGAGAAAGAGGCAAAAAGAGAATCTAGTGTTGTAAAAGCAGTTCCTTTAAGCAGAAAGAACAGCCACCTGTAGTGAAATTCTAGATATAATTCTCAAACATGGAGAACCTTCCAGATGTCTACCCTCACTGTACAATAGAACCTGATATTTTGGTTTCCCTGAAATTGCAGTCACCGTAGCACACAGACTTTGGTACAGATACTCTTCTGTGTGCTCTCAACCAAAAGGGACAGATGGCACTTTTCTTTATAGCTGCCCTGCACTGATGGGTGTTGTCCCATCAGTAGGTGTCTCCTCATTTCAGCTCGCCCGTTCCTGAGAAATAAGCACAGCACAGGGAGCTTCCCTGTGTGGCAATCACGTCTTCACCCAGGGCTGGATCACTGTGAAAGAAACTTTATGTTTATTTGTGTGTGTGTGTGTACATGTGTATGTGTGCATGGGTTCCTATAGAGGCCAGAGGAGGTCACTGAGTCCCTGGAGCTGCAGTTACAGGGATTTGTGACCCACAGGAAGTGAGTGCTGAGAACTAATTGCAAGAGCAGTAAACACTCTTAATAAGTGAGCCATCTCTCCACCCTCTTTATTTTATTTTTATTGTGGTGGGGTGGGGGTAGTGCATGTACCATAGTACATGCACCCTGTGGTAGTCCGAGGAAACCCTGTAGTTTGGTTCTCTCCTTCCACTTTTATGTGAATTCTAGAGATCAAATTCACGGTGGCAAGGTTGAGTTGCAAGTGTCTTACCACTGAGCCGTTCATCAGCTCATGGAGAAAATATTTTAAATTGTGGTATTTTTCTAACAACATCATGCCCAGCTCTAAGCAGTCCCTCCCTCAGGGCATGTGTATACTTCCTCTCTTGGAGTGTGATGCACCTTGCTAGTGTTTGCTGGCTGTGTGTGACATTTCTCTAGCAGACTGGGAAGTTTCAAAGTGCCTGGTCTGCCGGCGAGGGTGAATCCTCTTCCTTGCTCTCACAGTTCTCTGCCCTACTAGGGAGACACAGTCAGCTGTGCTTGCTTACCCCTTCTCTTCCTCACAAGGAGCTCCAGGAAAGCTGGCTTTCATCTTGCTTTGTGACAG
Seq C2 exon
GGCTCCTCTAGAACAGCACAGGACTCGGAAACCTCCCCAGTGTGGGATCTTGGCAGCTCCAGTCTGACACGTGCCCCATCTTTGACACCTGATTCTGAAGGGAAGAAACCTGCACAAGCTGTCAAAAAGGAGCCCAAGGAGCCCAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019122:ENSRNOT00000064083:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACCTGTCAGACACTCCCCTC
R:
TTCTTGGGCTCCTTGGGCTC
Band lengths:
214-1659
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]