RnoINT0138477 @ rn6
Intron Retention
Gene
ENSRNOG00000020138 | Slc4a3
Description
solute carrier family 4 member 3 [Source:RGD Symbol;Acc:3712]
Coordinates
chr9:82751637-82752300:+
Coord C1 exon
chr9:82751637-82751726
Coord A exon
chr9:82751727-82752133
Coord C2 exon
chr9:82752134-82752300
Length
407 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTTCCTTCCTGCCATTGCAGAAG
3' ss Score
9.27
Exon sequences
Seq C1 exon
GCTCGGCGCGTCATCGGGGACTTCGGCATTCCCATCTCCATCCTGGTGATGGTCCTTGTGGATTACTCTATCACAGACACCTACACACAG
Seq A exon
GTGAGCTTGCACCAATTCCCCTATGGCCGCTGCAAATTTCCACCAGCCCCAGGATCTGGAGCAGGGTTGCAGCCCAGCTCTCCTGGTTGAGTGGCAAGACGTCGGGCCACACCAGAGGCTGGACTACCCAGGGCATCTAACTGTGTATGATCCCAAACGGGAGGAATTTGGAAGAGTAAATACGAGCTGGTGCAGAGTGCCAGGTCTCTCCCACAGCAGGTCTCCTGACAGCTTCGAAGCTAGGGGGAAAGTATCCCATTGCTATGCCCTCAGCCAGCCCCTGGAATAGTGACTTTGGAGAATGACCTCAGAGCTCCGGGAATACTGTGGTAGGAACAGCTGCAATGTAGACCTCTTCTATGGGCAGCCTCTGGCTCTGACCCACGTCTTCCTTCCTGCCATTGCAG
Seq C2 exon
AAGCTGACGGTGCCTACAGGGCTCTCAGTGACTTCCCCGCATAAGCGCACGTGGTTCATCCCACCCTTGGGCAGTGCCCGCCCCTTCCCACCATGGATGATGGTGGCTGCTGCTGTCCCTGCACTCTTGGTCCTCATCCTGATATTCATGGAGACTCAGATCACTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020138:ENSRNOT00000027337:18
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=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=FE(9.7=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(18.4=100)
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:
CATCGGGGACTTCGGCATTC
R:
GCAGTGATCTGAGTCTCCATGA
Band lengths:
246-653
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]