RetrogeneDB ID:

retro_ptro_2918

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:9:122074169..122074543(-)
Located in intron of:ENSPTRG00000021342
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS25
Ensembl ID:ENSPTRG00000004361
Aliases:None
Description:Pan troglodytes ribosomal protein S25 (RPS25), mRNA. [Source:RefSeq mRNA;Acc:NM_001251993]


Retrocopy-Parental alignment summary:






>retro_ptro_2918
ATGCCACCCAAGGACTACAAGAAGAAGACAGACACTGGAAAGTCAGCCAAGAAAGACAAAGACCCAGTGAACAAACCCGG
GGGCAAGGCCAAAAAGAAGAAATGGTCCAAAGGCAAAGTTAGGGACAAGCTCAATACCTTGTCTTGTTTGACAAAGCTAC
ATATGACAAACTCTGTAAGGAAGTTCCCAACTATAAACTTGTAACTCCAGTTGTGGTCTCTAAGAGACTGAAGATTTGAG
GTTCCCTGGCCAGGGCAGCCCTTCTGGAGCTCCTTAGTAAAGGACTTATCAAACTGGTTTCAAAGCACAGAGCTCAAGTA
ATTTACACCAGAAATACCAAGGGCAGAGATGCTCCAGCTGCTGGTGAAGATGCA

ORF - retro_ptro_2918 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.48 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNL-VLFDKATYDKLCKEVPNYKLIT
MPPKD.KKK.D.GKSAKKDKDPVNK.GGKAKKKKWSKGKVRDKLN.L.VLFDKATYDKLCKEVPNYKL.T
RetrocopyMPPKDYKKKTDTGKSAKKDKDPVNKPGGKAKKKKWSKGKVRDKLNTL<VLFDKATYDKLCKEVPNYKLVT
ParentalPAVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA
P.VVS.RLKI.GSLARAAL.ELLSKGLIKLVSKHRAQVIYTRNTKG.DAPAAGEDA
RetrocopyPVVVSKRLKI*GSLARAALLELLSKGLIKLVSKHRAQVIYTRNTKGRDAPAAGEDA

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 .07 RPM 64 .85 RPM
SRP007412_cerebellum 0 .04 RPM 55 .74 RPM
SRP007412_heart 0 .03 RPM 84 .12 RPM
SRP007412_kidney 0 .00 RPM 127 .65 RPM
SRP007412_liver 0 .00 RPM 95 .88 RPM
SRP007412_testis 0 .00 RPM 59 .75 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2918 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2918 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2918 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4310
Gorilla gorilla retro_ggor_2880
Pongo abelii retro_pabe_3507

Parental genes homology:
Parental genes homology involve 10 parental genes, and 84 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000277722 retrocopies
Callithrix jacchus ENSCJAG000000136911 retrocopy
Dasypus novemcinctus ENSDNOG000000078807 retrocopies
Mus musculus ENSMUSG0000000992715 retrocopies
Oryctolagus cuniculus ENSOCUG0000001725611 retrocopies
Otolemur garnettii ENSOGAG000000072653 retrocopies
Pan troglodytes ENSPTRG00000004361 10 retrocopies
Sorex araneus ENSSARG000000022844 retrocopies
Tupaia belangeri ENSTBEG0000001024416 retrocopies
Tarsius syrichta ENSTSYG0000000542215 retrocopies



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