RetrogeneDB ID: retro_pabe_2006

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:78379399..78379641(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V0E1
• Ensembl ID: ENSPPYG00000029669
• Aliases: None
• Description: V-type proton ATPase subunit e 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5RAV0]

Sequence

>retro_pabe_2006
ATGGTATATCAGGGCCTCACCATACCTCTCATTGCAATGAGCGTGTTTTGGGGCTTCACTGATTTCTTCATGCCTTGGTT
CATCCCTAAGGGTCCCAACTAGGGAGTTATCATTACCATTTTGGTGACCTGTTCAGTTTGTTGCTGTCTCTTTTGGCTGA
TTGCAATCCTGGCCAACTCAACCCTCTCTTCAGACTGCAGTTGAAACATGAAATCATGTGGTGTCTGAAGTGTCATTGGC
CT

Alignment

ORF - retro_pabe_2006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAYHGLTVPLIVMSVFWGFVGFLVPWFIPKGPNRGVIITMLVTCSVCCYLFWLIAILA-QLNPLFGPQLK
          M.Y.GLT.PLI.MSVFWGF..F..PWFIPKGPN.GVIIT.LVTCSVCC.LFWLIAILA.QLNPLF..QLK
Retrocopy MVYQGLTIPLIAMSVFWGFTDFFMPWFIPKGPN*GVIITILVTCSVCCCLFWLIAILA<QLNPLFRLQLK

Parental  NETIWYLKYHWP
          .E..W.LK.HWP
Retrocopy HEIMWCLKCHWP

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	24.83 RPM
SRP007412_cerebellum	0.00 RPM	15.69 RPM
SRP007412_heart	0.00 RPM	44.10 RPM
SRP007412_kidney	0.00 RPM	180.65 RPM
SRP007412_liver	0.00 RPM	115.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2006 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2006 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2006 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2090
Pan troglodytes	retro_ptro_1537
Gorilla gorilla	retro_ggor_1632
Macaca mulatta	retro_mmul_983
Callithrix jacchus	retro_cjac_1296

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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,