RetrogeneDB ID: retro_ptro_2190

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:133604189..133604412(+)
• Located in intron of: ENSPTRG00000017228

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V0E1
• Ensembl ID: ENSPTRG00000017538
• Aliases: ATP6V0E1, ATP6V0E
• Description: None

Sequence

>retro_ptro_2190
TATCATGGCCTCACAGTGACGAGCATGTTCTGGGGCTTTGTTGGCTTCTTTGTGCCCTAGTTCGTCCCTAAGCGGCCTAA
CTGGGGAGTTATCATCACCATGATGGTGACCTGTTCAGTTTGCCACTCTCTTTTGGCTGATTGCAATTTTGGCCCAATGC
AACCCTCTCTATAGACCATGACTGAAAGATGAAACCACCTGGTATCTGAAGCATCATTGGCCT

Alignment

ORF - retro_ptro_2190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.5 %
• Parental protein coverage: 97.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YHGLTVPLIVMSVFWGFVGFLVPWFIPKGPNRGVIITMLVTCSVCCY-LFWLIAILAQLNPLFGPQLKNE
          YHGLT....V.S.FWGFVGF.VP.F.PK.PN.GVIITM.VTCSV.C..LFWLIAILAQ.NPL..P.LK.E
Retrocopy YHGLT----VTSMFWGFVGFFVP*FVPKRPNWGVIITMMVTCSV-CH>LFWLIAILAQCNPLYRP*LKDE

Parental  TIWYLKYHWP
          T.WYLK.HWP
Retrocopy TTWYLKHHWP

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	0.04 RPM	18.36 RPM
SRP007412_cerebellum	0.14 RPM	11.40 RPM
SRP007412_heart	0.00 RPM	43.57 RPM
SRP007412_kidney	0.00 RPM	127.49 RPM
SRP007412_liver	0.03 RPM	76.93 RPM
SRP007412_testis	0.00 RPM	26.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2190 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2190 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2190 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3240
Gorilla gorilla	retro_ggor_2206
Pongo abelii	retro_pabe_2688
Callithrix jacchus	retro_cjac_1923

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015183	1 retrocopy	retro_acar_192,
Ailuropoda melanoleuca	ENSAMEG00000011283	1 retrocopy	retro_amel_1124,
Bos taurus	ENSBTAG00000015100	4 retrocopies	retro_btau_1320, retro_btau_1428, retro_btau_369, retro_btau_653,
Canis familiaris	ENSCAFG00000031898	3 retrocopies	retro_cfam_1530, retro_cfam_1961, retro_cfam_1996,
Choloepus hoffmanni	ENSCHOG00000004421	9 retrocopies	retro_chof_1269, retro_chof_1600, retro_chof_1795, retro_chof_1856, retro_chof_2141, retro_chof_2270, retro_chof_2440, retro_chof_718, retro_chof_779,
Callithrix jacchus	ENSCJAG00000019225	4 retrocopies	retro_cjac_1296, retro_cjac_1616, retro_cjac_1923, retro_cjac_2873,
Felis catus	ENSFCAG00000031789	1 retrocopy	retro_fcat_1282,
Homo sapiens	ENSG00000113732	3 retrocopies	retro_hsap_2090, retro_hsap_2780, retro_hsap_3240,
Gorilla gorilla	ENSGGOG00000006701	3 retrocopies	retro_ggor_1632, retro_ggor_1937, retro_ggor_2206,
Macropus eugenii	ENSMEUG00000008589	3 retrocopies	retro_meug_1213, retro_meug_1393, retro_meug_530,
Myotis lucifugus	ENSMLUG00000009804	2 retrocopies	retro_mluc_1749, retro_mluc_628,
Macaca mulatta	ENSMMUG00000013825	2 retrocopies	retro_mmul_1446, retro_mmul_983,
Oryctolagus cuniculus	ENSOCUG00000006174	2 retrocopies	retro_ocun_1653, retro_ocun_732,
Otolemur garnettii	ENSOGAG00000017071	2 retrocopies	retro_ogar_1368, retro_ogar_529,
Ochotona princeps	ENSOPRG00000000673	1 retrocopy	retro_opri_1191,
Pongo abelii	ENSPPYG00000029669	3 retrocopies	retro_pabe_2006, retro_pabe_2236, retro_pabe_2688,
Pan troglodytes	ENSPTRG00000017538	3 retrocopies	retro_ptro_1537, retro_ptro_1881, retro_ptro_2190 ,
Rattus norvegicus	ENSRNOG00000003269	1 retrocopy	retro_rnor_1498,
Sarcophilus harrisii	ENSSHAG00000007047	1 retrocopy	retro_shar_556,
Tupaia belangeri	ENSTBEG00000005462	1 retrocopy	retro_tbel_3475,
Tarsius syrichta	ENSTSYG00000006590	5 retrocopies	retro_tsyr_1387, retro_tsyr_1422, retro_tsyr_1971, retro_tsyr_2020, retro_tsyr_547,
Tursiops truncatus	ENSTTRG00000010626	5 retrocopies	retro_ttru_1411, retro_ttru_1656, retro_ttru_1891, retro_ttru_250, retro_ttru_365,
Vicugna pacos	ENSVPAG00000011996	1 retrocopy	retro_vpac_622,