RetrogeneDB ID: retro_ptro_2168

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:96476409..96476660(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX19
• Ensembl ID: ENSPTRG00000041621
• Aliases: None
• Description: cytochrome c oxidase assembly homolog 19 (S. cerevisiae) [Source:HGNC Symbol;Acc:28074]

Sequence

>retro_ptro_2168
ATGTCCACAGCCATAAATCTTAGGACCAAGATCTTCCAGGCATGGCCCCTGGACAAGGGCAGCTTCCCACTGAAACTTTT
CAATAAATATAAAAGCTTAAAGAGAAATTTATGAGGTGCCTTCATGATAATAAATGTAAACATATTTTGCAGAAGAATAA
ATCAAAAGCATATTCAGAATGCAGAATGGAGAGACAACAAAAGGTGTAAAAACCAAGAGGAACACTAGGATTTGGAGATT
TGATAGAAAAT

Alignment

ORF - retro_ptro_2168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.59 %
• Parental protein coverage: 68.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTAMNFGTKSFQPRPPDKGSFPLDHLGECKSFK-EKFMKCLHNNNFENALCRNESKEYLECRMERSRLG
          MSTA.N..TK.FQ..P.DKGSFPL......KS.K.EKFM.CLH.N.....L..N.SK.Y.ECRMER....
Retrocopy MSTAINLRTKIFQAWPLDKGSFPLKLFNKYKSLK<EKFMRCLHDNKCKHILQKNKSKAYSECRMERQQKV

Parental  LLHSGRLHLPELLGN
          ....G.L....L..N
Retrocopy *KPRGTLGFGDLIEN

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	135.15 RPM
SRP007412_cerebellum	0.00 RPM	35.81 RPM
SRP007412_heart	0.00 RPM	3.67 RPM
SRP007412_kidney	0.00 RPM	8.11 RPM
SRP007412_liver	0.00 RPM	22.00 RPM
SRP007412_testis	0.00 RPM	2.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2168 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2168 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3300
Gorilla gorilla	retro_ggor_1312
Macaca mulatta	retro_mmul_2067

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015253	1 retrocopy	retro_btau_671,
Homo sapiens	ENSG00000240230	1 retrocopy	retro_hsap_3300,
Gorilla gorilla	ENSGGOG00000034907	1 retrocopy	retro_ggor_1312,
Macaca mulatta	ENSMMUG00000007202	1 retrocopy	retro_mmul_2067,
Pan troglodytes	ENSPTRG00000041621	1 retrocopy	retro_ptro_2168 ,
Pteropus vampyrus	ENSPVAG00000002192	1 retrocopy	retro_pvam_409,
Tursiops truncatus	ENSTTRG00000011489	2 retrocopies	retro_ttru_1140, retro_ttru_1270,