RetrogeneDB ID:

retro_ptro_2440

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:70389210..70389495(-)
Located in intron of:ENSPTRG00000018327
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL37
Ensembl ID:ENSPTRG00000016822
Aliases:None
Description:Pan troglodytes ribosomal protein L37 (RPL37), mRNA. [Source:RefSeq mRNA;Acc:NM_001246471]


Retrocopy-Parental alignment summary:






>retro_ptro_2440
AAGGGAACGCCATCGTTTGAAAAGTGTCTCAATAAGACGCACACATTGTGCCACCACTGTGGCTCTAAGGCCTGCCACCT
TCAGAGGTCATCCTGTGGCAAATGTGGCTACCCTGCTAAGTGCAAGAGGAAGTATAACTGAAGTGCCAAGGCTTAAAGAT
GAAATAATACCAGGACTGGTCGAGTGAGGCACCTGAATATTGTATACCGCAGATTCAGGCGTGGATTCTGAGAAGGAACA
ACATCTAAACCCAAGAGGGCAGCTGTTGTAGCATCCAGTTTATCT

ORF - retro_ptro_2440 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.84 %
Parental protein coverage: 97.94 %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGRMRHLKIVYR
KGT.SF.K..NKTHTLC..CGSKA.HLQ.S.CGKCGYPAK.KRKYN.SAKA.R.N.T.TGR.RHL.IVYR
RetrocopyKGTPSFEKCLNKTHTLCHHCGSKACHLQRSSCGKCGYPAKCKRKYN*SAKA*R*NNTRTGRVRHLNIVYR
ParentalRFRHGFREGTTPKPKRAAVAASSSS
RFR.GF.EGTT.KPKRAAV.ASS.S
RetrocopyRFRRGF*EGTTSKPKRAAVVASSLS

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 186 .20 RPM
SRP007412_cerebellum 0 .00 RPM 129 .27 RPM
SRP007412_heart 0 .00 RPM 107 .00 RPM
SRP007412_kidney 0 .03 RPM 357 .44 RPM
SRP007412_liver 0 .00 RPM 210 .97 RPM
SRP007412_testis 0 .00 RPM 46 .90 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2440 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2440 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2440 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3610
Gorilla gorilla retro_ggor_2436
Pongo abelii retro_pabe_2962

Parental genes homology:
Parental genes homology involve 11 parental genes, and 117 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG0000014559221 retrocopies
Latimeria chalumnae ENSLACG000000027871 retrocopy
Loxodonta africana ENSLAFG0000003005213 retrocopies
Myotis lucifugus ENSMLUG0000000156510 retrocopies
Macaca mulatta ENSMMUG000000238076 retrocopies
Monodelphis domestica ENSMODG000000203013 retrocopies
Nomascus leucogenys ENSNLEG000000165084 retrocopies
Otolemur garnettii ENSOGAG000000343007 retrocopies
Pongo abelii ENSPPYG0000001542226 retrocopies
Pan troglodytes ENSPTRG00000016822 20 retrocopies
Rattus norvegicus ENSRNOG000000125386 retrocopies



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