RetrogeneDB ID: retro_ptro_2765

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:74605871..74606492(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MRPL9
• Ensembl ID: ENSPTRG00000001295
• Aliases: None
• Description: None

Sequence

>retro_ptro_2765
TGGAAGGTACCACTGGCCAGGGAGGGCCAGAAGCTGTGTCTGCACCAGCGACACTACATCGAAAAGCTGGTGGAGGACAC
GGAGCACTGGCCCAAAGAAAACCTGGAGATCATCTTCACACAGTCTGTGGAGACACTTGGAGTCCGGGGTGACCTGATCT
CAGTAAAGAAATCTGTGGATCGGAATCAACTCCTTTCTCAGAGACTGGCTGCATATGCATCACCTGAAAACAAGAAGCTG
TTTGAAGAGGAGAAATTGCTGAGACCAGGAGGAAAGTTAGAGAAGATCCAGACCAAGGCAGGTGAGGCAACAGTGACATT
TCTGAAAAGCTGTCACCTGGAGGTAGGGATGAAGAACAGTGTCAAACGGGAGCTGAACCCTGACACAGTTGCCTGCCACT
TCTTCAAGAATCTTGGTGGTGTGGTCACCCCCCATATATTAAAATTACCAGAAGAGCCCCTCACTCGGTGGGGCAAGTAC
TGTTGTGAGGTGACGGTAAATGGGCTTGGTACTGTGAGGGTGCCTATGTCTCTGGTAAACTTTGAGAGGCCCAAAATCCA
AAGTTAGAAGTACTGGTTAGCCCAGCAAGCGGCCAAGGGCATGGCCCCACCAGCCCCTAGA

Alignment

ORF - retro_ptro_2765 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.81 %
• Parental protein coverage: 77.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WKVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGRNRLLPQGLA
          WKVPLA.EG.K..LH.RH...KLVEDT.H.PKENLE.I.TQSVE..GVRGDL.SVKKS..RN.LL.Q.LA
Retrocopy WKVPLAREGQKLCLHQRHYIEKLVEDTEHWPKENLEIIFTQSVETLGVRGDLISVKKSVDRNQLLSQRLA

Parental  VYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNVKWELNTEIVARHFFKNLGV
          .YASPENKKLFEEEKLLR..GKLEKIQTKAGEATV.FLKSC.LEVGMKN.VK.ELN...VA.HFFKNLG.
Retrocopy AYASPENKKLFEEEKLLRPGGKLEKIQTKAGEATVTFLKSCHLEVGMKNSVKRELNPDTVACHFFKNLGG

Parental  VVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNFEKPKTKRYKYWLAQQAAKAMAPTSPQ
          VV.PH.LKLPEEP.TRWG.Y.CEVTVNGL.TVRVPMS.VNFE.PK....KYWLAQQAAK.MAP..P.
Retrocopy VVTPHILKLPEEPLTRWGKYCCEVTVNGLGTVRVPMSLVNFERPKIQS*KYWLAQQAAKGMAPPAPR

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	27.08 RPM
SRP007412_cerebellum	0.00 RPM	37.10 RPM
SRP007412_heart	0.00 RPM	20.05 RPM
SRP007412_kidney	0.00 RPM	27.75 RPM
SRP007412_liver	0.00 RPM	29.20 RPM
SRP007412_testis	0.00 RPM	28.24 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2765 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2765 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2765 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4078
Gorilla gorilla	retro_ggor_2735
Pongo abelii	retro_pabe_3347

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000258	1 retrocopy	retro_chof_10,
Dasypus novemcinctus	ENSDNOG00000011403	1 retrocopy	retro_dnov_1989,
Homo sapiens	ENSG00000143436	1 retrocopy	retro_hsap_4078,
Gorilla gorilla	ENSGGOG00000001902	1 retrocopy	retro_ggor_2735,
Loxodonta africana	ENSLAFG00000006271	2 retrocopies	retro_lafr_498, retro_lafr_563,
Nomascus leucogenys	ENSNLEG00000010275	1 retrocopy	retro_nleu_2045,
Oryctolagus cuniculus	ENSOCUG00000001383	1 retrocopy	retro_ocun_725,
Otolemur garnettii	ENSOGAG00000030456	1 retrocopy	retro_ogar_159,
Pongo abelii	ENSPPYG00000000857	1 retrocopy	retro_pabe_3347,
Pan troglodytes	ENSPTRG00000001295	2 retrocopies	retro_ptro_2765 , retro_ptro_2996,