RetrogeneDB ID: retro_ptro_2996

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL390842.1:3607..4235(-)
• 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_2996
GAGCACTGGGTGATGGAAGTACTCTGGCAGGGAGGCCAGAAGCTGTGTTTGCACCAGCGACACTACATTTAAAGCTTGTG
GAGGACACGGAGCCCCTGCCCCAAGAAAACTGGAGATCATCTTCACACAGTCTGTGGAGACACTTGGAGTCCGGGGTGAC
CTGATCTCAGTAAAGAAATCTGTGGATCGGAATCAACTCCTTTTTTAGAGACTGGCTGCATATGCATCACCTGAAAACAA
GAAGCTGTTTGAAGAGGAGAAATTGCTGAGACCAGGAGGAAAGTTAGAGAAGATCCAGACCAAGGCAGGTGAGGCAACAG
TGACATTTCTGAAAAGCTGTCACCTGGAGGTAGGGATGAAGAACAGTGTCAAACGGGAGCTGAACCCTGACACAGTTGCC
TGCCACTTCTTCAAGAATCTTGGTGGTGTGGTCACCCCCCATATATTAAAATTACCAGAAGAGCCCCTCACTCGGTGGGG
CAAGTACTGTTGTGAGGTGACGGTAAATGGGCTTGGTACTGTGAGGGTGCCTATGTCTCTGGTAAACTTTGAGAGGCCCA
AAATCAAAAGATAGAAGTACTGGTTAGCCCAGGAAGCTGCCAAGGGCATGGCCCCACCAGCCCCTAGA

Alignment

ORF - retro_ptro_2996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.17 %
• Parental protein coverage: 78.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERWWKVPLAGEGRKPRLHRRHRV-YKLVEDTKHRPKEN-LELILTQSVENVGVRGDLVSVKKSLGRNRLL
          E.W....L...G.K..LH.RH....KLVEDT...P.EN.LE.I.TQSVE..GVRGDL.SVKKS..RN.LL
Retrocopy EHWVMEVLWQGGQKLCLHQRHYI<LKLVEDTEPLPQEN<LEIIFTQSVETLGVRGDLISVKKSVDRNQLL

Parental  PQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNVKWELNTEIVARHFF
          ...LA.YASPENKKLFEEEKLLR..GKLEKIQTKAGEATV.FLKSC.LEVGMKN.VK.ELN...VA.HFF
Retrocopy F*RLAAYASPENKKLFEEEKLLRPGGKLEKIQTKAGEATVTFLKSCHLEVGMKNSVKRELNPDTVACHFF

Parental  KNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNFEKPKTKRYKYWLAQQAAKAMAPTS
          KNLG.VV.PH.LKLPEEP.TRWG.Y.CEVTVNGL.TVRVPMS.VNFE.PK.KR.KYWLAQ.AAK.MAP..
Retrocopy KNLGGVVTPHILKLPEEPLTRWGKYCCEVTVNGLGTVRVPMSLVNFERPKIKR*KYWLAQEAAKGMAPPA

Parental  PQ
          P.
Retrocopy PR

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_2996 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2996 has 0 orthologous retrocopies within eutheria group .

---

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 ,