RnoINT0138486 @ rn6
Intron Retention
Gene
ENSRNOG00000020138 | Slc4a3
Description
solute carrier family 4 member 3 [Source:RGD Symbol;Acc:3712]
Coordinates
chr9:82745029-82746722:+
Coord C1 exon
chr9:82745029-82745225
Coord A exon
chr9:82745226-82746573
Coord C2 exon
chr9:82746574-82746722
Length
1348 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
CAAGTCCACCTTGTCCACAGGTC
3' ss Score
8.36
Exon sequences
Seq C1 exon
CTCCCCCAGTCCCCGGGCCCGGGCTTCCCGAATCTCTACAGAGAAGAGTCGACCCTGGAGTCCATCAGCCAGCTATGACCTGCGGGAGCGATTGTGCCCAGGCAGTGCCCTGGGCAACCCTGGGCCAGAGCAGCGGGTGCCCACTGATGAGGCGGAGGCTCAAATGCTGGGTTCTGCCGATCTGGACGACATGAAGA
Seq A exon
GTGAGTGAGACCCTGTGGCAGAGAGAGCTTAATTCGACTAAGCCACCTCTCTGCCAGAGCTTTTCCCTTAGTGTCACTCAGGAGTGCTGTCTGAGCCACCTACTGCATAAATCCACCCTGTTCCACACACACTCCTGGAGGAGAGCTCTCCTAAGGCCTCCCGCCTTTATAAACTCTACGCTAACCCACTTGCCTGGAGGCTGAGGGCTGAGCTGCCCTGCCGGCCCCTTCTCCCCAAGCCAGGCCTGCTGCTACCCTCACTCCTTCCTACCACCCTTGCCCTGGCCTGGCTGTGATCTCGGCACATTCCTTCCATCTTATCAGTGCCTGGCTCTGGTGCCACCTGTCATCACCCACGGGGCTCTGTGCCCAGGCTAGGGGCATCACTGGTCTCCTGCCTCCTCCTCCTCCTAAGGTTCACAGGGTGTGGGCGGGGGCAGAGGGGGGGGAGTTAGGGCTTTGAGCTCAATACGTCATGGAAAGTTGCCAGGGCCTGAGGACAGGGACAGGAACAATCCGATGGCAGCAGCAGTGGGATTGGGGGAGTCATAGGGAGGGTGTATATAGGGGGACAAGGAGAGTTGGGAGCAGGAAACCTTACCACGTCCAGCTCTGTGTGGGCAAAGGCAGTTCCGGTAGGGTCTCCCACTTTTTGGGACAGCCAGGACTGAGGCCTTGGCCACCAGGGGAATGACAAGCCCTCTGGACAAGGTCATGGAGCCCAATGGAGCTCTGGGTCCTAAGCCTGGGGACACTGAAGACCGAGGCCCTGGGAGGAATCCAGCCCCTGGCACTGGTGACTTAGTGGCCTCAGAGGATTTGGAAATGTTTGTACTGGACTTTGAAGACTATGGCCTGTGGGAGCCCATGAGGGGCCACCCGAGCCCCCTGGCAGGGGTAGCTGCTTGTGAGTAACTGGGCAGCTAGCCTCTCTCCAGCTGTTCATCTGGGCAGGGCAGGTGGGAGGGTAACCAAGCGGCCCTTATAAACTTGCTTGATGGGCACTAGTGGGTCTGGGAATTGGGTGCTGTGGTTATGAAAGTGTTGGGAGCTAGGTGTCTAGGGGCCAGCATTGAACCCATGGCCCCACAGGTTGTGTCAGGGGCTTTAGGGTATAGATGGGGCTGAAAGCTTAAGTGGGATCTGGCTTTTGTTGTGACTTGGCCAGTGCTACAGTGTTGCTTTGTACTGTCTGAGACATTGTCGCCACATCTGTGAAATGGCTACCTGGATAATGTGTACGGGATAACAACCTGGACCTGGTGGGTACAAAAGGGGCCTAGAGCATGTGGGCTGTGATCATGACCTAGAGATGGATCCTTGGAGTCCAAGTCCACCTTGTCCACAG
Seq C2 exon
GTCATCGGCTGGAGGACAACCCCGGAGTGCGGCGACACTTGGTGAAGAAACCATCCCGGATACAGGGTGGGAGAGGCAGCCCCAGTGGCCTGGCGCCCATCTTGCGCAGGAAAAAGAAGAAGAAGAAGCTGGATCGGAGGCCTCATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020138:ENSRNOT00000027337:6
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=0.870
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
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGCTTCCCGAATCTCTACAG
R:
CTCATGAGGCCTCCGATCCAG
Band lengths:
326-1674
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]