RnoINT0137913 @ rn6
Intron Retention
Gene
ENSRNOG00000004966 | Slc38a11
Description
solute carrier family 38, member 11 [Source:RGD Symbol;Acc:1306005]
Coordinates
chr3:51414065-51416183:-
Coord C1 exon
chr3:51416063-51416183
Coord A exon
chr3:51414140-51416062
Coord C2 exon
chr3:51414065-51414139
Length
1923 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGC
5' ss Score
8.89
3' ss Seq
GGGGCATTTTGTTTTTCCAGGAT
3' ss Score
7.21
Exon sequences
Seq C1 exon
AGAGAGACAGACCCGAGTGACAGAGAGAGCCTGGTCTCCGGACATGAACACGGAGGGAAATCGAGTCAGTCTGCAGCTGTTTTCAATGTAGTCAATTCTGTTATAGGATCTGGGATAATAG
Seq A exon
GTAAGCCACCTGTGTCTGCTTGGTTCTGTTTATGAAGTAAAAAGACCAGCTTTTCAAAGTGTTACTGTTATTCTAGGATTTTCTCAGACTTCAATGGGGAGATTGGTGGTTTTCTTCCATAAAAGCCATTCTATTTATTTTTCCATAGTAATGTTCCATCCTCTTTATGTGAAGCTGCACTGTTTCCCTCCATGGCAGACAATAGCGTCCTCCAGTTGGAGGGAGGGGCTGCACAGGAGCTGGGGAAACTGGCTTTCATAGGTTGCCTGATCAGTGGATCCTTTCAACTAGAGCATTTGCTTCTTCCTTCTGAAGTAGAATCTATTACAAAAATCATCTTAATATCAGTGTGAAACTTGAGGATTCTTGCATATACTAAGTGTACAAAAGTTTAATGTGAGACTTTTAAGAATCCTATGAAAATTAAACTAGATAATATCTCCTTGTGCACCTATGTGACCTTAAATTTAAAAATGTGAACTTATGAAATCCTTTCTTCAATCTAGTCATTAATATAGTTCATTCACAACAGTGTTTACAATTGGTAAGAATAGTCTATGTTATTCCACTAAGTTAGAAGCAAGGAAAAGCTTCTAAAAAAGTAAAAACGTTTAAAGGTATTCCATTCCATTAATAGAAGCAGTATTTTCCAGTGTTTGTTATTCTTTTTGTAGTTGGAAACATTCCATTTCCCAAAAGGCAGGGAAGACAAAAACCTATCTATTGCAATGCCCACCAAATATGTAACTTTTCGATTACAAAATTTCCAGATTTTAATTTACTTAAAAGTGTAAGTTTATCAAATGGATCCTTTTTATTTATTATTTCATTCTATGTGCATGTATAGGTGTTTTGCCTGAATGCATATATACCACATGTGTGCCTGGTGCCCACAGAGATCAGCAGAGGGTGTCTGGTAACCTGGAATAGGAGTTCCAGGATGGCTGTGAGTCGCCATGTGGGTGAGGGAGATGGGTGTTTGGTAAGAGCAGCAAGGGCTCTAATGGCTGAGCCTTCTCTCTAGTCCCTGAGATAAGTTCCCGACATTTTTTTTTTTCACAAGGTGCTGTGATTTCTGGCTTTGCCTTAATCCATATACATGTTTTTTAAATGAACAATAATTTGTAGGTTCCTGGAGTGAAACAGAAACAAGCAGGGCACACGCCTGTTTGGAAGCCTGTCTCCATGTATCACAGGAATATGGACAGTTCAACCTGACAGAATTCTAGAATTTACTCCTCATGTGAATACTTTTCCAGGTTAATCTTAGTCAGCGATGCCGAAATGTTCCCCTTCAGTACCCTCAGCAGAGTTATTTAAAAGAGAAATCTTTTTTTTTTCTGAAAAATGAAATGCTTAAATTAATTTATTTTGGATATTTTATAGTCTGTAATCTAAAATGACCCCTAGGTACAAAGCAGTAAAAAATCATGTTATAGACCCCACTTGGCTCGAGAAGAAGTAATTGCTTGCCAGTTCCTCCGCATTCTCTCTATTTTTTACATCGTCCCCCCATTTTGACTCCAGAACCAGTTTTCCCTAAGATCCTGCAACTGTTCCCTGGTGCTTTCCATAGCAGCATAGAAGGAAGGGGGCTTCATCCTCCACCGAGTCCAGGGCACTAACCGTCACCCTGAGAGAAGCATTGTTTATGTGACCTGGAATCAGTTTTTCATTTGCTGCTTTTTAATTCTTCCATCGTCTCATGTGCTTGCTTTCTTGACAGGTCCTTAACTTAATGACATTCCATTCTGAAATACGAGCTAATATGCTTATATTTGATTTTTGACTACCCACCCCACCTTGCAACTTTTAAATCACTTACATAGTTTATTTTACCATGTATGAATTGCAAGAGATTTTTTTTTTTTGCATTTCCGATATGTCTTTTTAACGTGAGATTGGGGCATTTTGTTTTTCCAG
Seq C2 exon
GATTGCCCTATTCAATGAAGCAAGCCGGATTTCCCTTGGGAATACTGCTTTTATTCTGGGTCTCATACATCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004966:ENSRNOT00000006634:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.390 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0149013=Aa_trans=PU(22.9=53.7)
A:
NA
C2:
PF0149013=Aa_trans=FE(26.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGACCCGAGTGACAGAGAG
R:
CTGTGATGTATGAGACCCAGAA
Band lengths:
190-2113
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]