RetrogeneDB ID:

retro_sscr_120

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:1:103537751..103538265(+)
Located in intron of:ENSSSCG00000021383
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL10A
Ensembl ID:ENSSSCG00000001543
Aliases:None
Description:Sus scrofa ribosomal protein L10a (RPL10A), mRNA. [Source:RefSeq mRNA;Acc:NM_001097477]


Retrocopy-Parental alignment summary:






>retro_sscr_120
ACAGACGCTTCTCGGGCACCTCAGGCCTAAGTCTACTCCCCGCCCCAAGTTCTCCGTTTGTATTCTGGGAGACCAGCAGC
ATTGTGATGAGGCCAAGGCTGTGGATATCCCACACATGGACATCGAGGCACTGAAGAAACTCAACAAGAATAAGAAACTG
GTCAAGAAGCTGGCCAAGAAGTATGATGCCTTTTTGGCTTCAGAGTCTCTAATCAAGCAGATTCCATGAATCCTGGGCCC
TGGCCTGAATAAGGCTGGCAAGTTCCCTTCCTTGCTGACCCACAATGAGAATATGGTGGCCAAAGTTGATGAAGTGAAGT
CCACGATCAAGTTCCAGATGAAGAAGGTGCTGTGTCTCGAAGTGGCTATTGGCCACGTGAAGACGACAGATGATGAGCTT
GTGTATAACATCCTTTTTGCTGTCAACTTCCTGGTGTCATTGCTCAAGAAAAATTGGCAGAACGTCTGAGCTTTGTACAT
TAAGAGCTCCAGGGGCAAATGCCAGCACCTGTAC

ORF - retro_sscr_120 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.23 %
Parental protein coverage: 97.16 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTNASRAP-SGLSLL-PAP-FSVCVLGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLAS
T.ASRAP.SGLSLL.P.P.FSVC.LGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLAS
RetrocopyTDASRAP<SGLSLL<PRPKFSVCILGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLAS
ParentalESLIKQIPRILGPGLNKAGKFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNI
ESLIKQIP.ILGPGLNKAGKFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCL.VA.GHVK.TDDELVYNI
RetrocopyESLIKQIP*ILGPGLNKAGKFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCLEVAIGHVKTTDDELVYNI
ParentalHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQRLY
..AVNFLVSLLKKNWQNV.ALYIKS..GK.Q.LY
RetrocopyLFAVNFLVSLLKKNWQNV*ALYIKSSRGKCQHLY

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP014902_placenta 0 .27 RPM 412 .66 RPM
SRP014902_testis 0 .14 RPM 595 .91 RPM
SRP018288_heart 0 .47 RPM 480 .18 RPM
SRP018288_kidney 0 .49 RPM 296 .50 RPM
SRP018288_liver 0 .96 RPM 235 .55 RPM
SRP018288_lung 0 .61 RPM 299 .98 RPM
SRP018856_adipose 0 .31 RPM 773 .63 RPM
SRP035408_brain 0 .06 RPM 256 .82 RPM
SRP035408_liver 0 .06 RPM 287 .98 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_120 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_120 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_120 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000194944 retrocopies
Dasypus novemcinctus ENSDNOG000000129213 retrocopies
Equus caballus ENSECAG000000140902 retrocopies
Macropus eugenii ENSMEUG000000057606 retrocopies
Microcebus murinus ENSMICG000000124583 retrocopies
Monodelphis domestica ENSMODG000000137662 retrocopies
Mus musculus ENSMUSG000000378058 retrocopies
Ornithorhynchus anatinus ENSOANG000000145741 retrocopy
Pongo abelii ENSPPYG0000001652910 retrocopies
Sarcophilus harrisii ENSSHAG000000020471 retrocopy
Sus scrofa ENSSSCG00000001543 7 retrocopies



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