RnoINT0138468 @ rn6
Intron Retention
Gene
ENSRNOG00000020138 | Slc4a3
Description
solute carrier family 4 member 3 [Source:RGD Symbol;Acc:3712]
Coordinates
chr9:82741920-82743114:+
Coord C1 exon
chr9:82741920-82742582
Coord A exon
chr9:82742583-82742971
Coord C2 exon
chr9:82742972-82743114
Length
389 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGT
5' ss Score
9.65
3' ss Seq
CCCCGCCCTCCTTCCCCAAGGCT
3' ss Score
8.45
Exon sequences
Seq C1 exon
CCCTTTGTGTATTCTAAGGTGTAGGGGCATGGCTTAAACTGACTGTCATTTTCAAGGCTTTTATGGGCATGGCTATGCTAGGTGCCCAGTTTCAGAGACTCAGAAAACACACTGGGGTCCAGGTGCCCTTTCCCAAGATCTCTCTGACCTTGGAAAGTGAGATAGGTCCTCTACGTTTGGAGAAGAGCTGGGTGGGGGTGGGTGTTGGGCAGAGGAACGGTGTGGAAACTTAGCCCACAGGATTTTACAGTGGTTGGCCCAATTGGAATGCCCCTGTTTCAGCTGCCTCTGGCTACAGATGGGTAGATACTGTGCCAAGGTCAAATGTTGGGTGGCACCCAGCGCCAGAAGCCAGGCCTTTGAAGGGCATCAGCTGAACTGGAGGTGTTGATGGCAAATGCTTTCAGGGGTCTGTGATCTTGGAAACGGGCCCAAGCTGGAGAGGCTTGTTTGCGCGAAGAGGGTCTCCTCCAGGGCTCCTGAGGGAAAGGGAGGGGTGGCTAAAAGCAAGGTGGAGGAGTGCGTTTGAGGGATTGTGGGAATTTAGGGCCGTGCACCCGCCCCTCCTCCCCCCGCAATGCGTGGGGCGCCTGGAAAGGGGTCTTGCGGGCAGGTGGGATCCTGCGGGGACCCGAGCGCCGGGCCCATGCTGGCCCAGTCGGG
Seq A exon
GTAAGTCAGGAATCGTCCACTCCCATTGTGCGGCCGGGCGGCGGCCGGCTGGCAGAGCCGAGCTCTAGGAGGTGGAGCCGTGGACTGCGGGCTCCGGCGCCTGCGTCCGACCTGCCCGGCTCTGCGCGGCGAGAGGCCGGACGGGAACCCGGCAGCCGCGCCCCGGCGCTAGCGGGGAGGGACATGGGGCGCGGCGGTTCTCCCAAGCCCCGCAGGTTCCGGAGCCCGGAGGTACTTAAGGGCAAGGCGTGGGCCGCGGGCCTGGTGGGGACATCGGACTAACCTGGACCGGGTTGGGCCTCGGAAGTGAGAGCGGGCTGGGCACGGGGATGGAGTACCCCGGAGGGGGCCCACCAGCGCGATTATTGACCCCGCCCTCCTTCCCCAAG
Seq C2 exon
GCTCCCCAAGAGGTCTCCGCAGCGCCCCCTTCTTCTCACCCAGGATTTGGGTCCCGTAGTGACTGAGAGACTCCTAAGTCTTCAGCCCAACCATGGCTAATGGGGTGATCCCACCGCCCGGGGGCGCCTCCCCCCTACCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020138:ENSRNOT00000027337:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=1.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGCAAATGCTTTCAGGGGT
R:
CTCTCAGTCACTACGGGACCC
Band lengths:
342-731
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]