RetrogeneDB ID: retro_cjac_1923

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:72507509..72507714(-)
• Located in intron of: ENSCJAG00000013322

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V0E1
• Ensembl ID: ENSCJAG00000019225
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e1 [Source:HGNC Symbol;Acc:863]

Sequence

>retro_cjac_1923
ATGAGCATGTTCTGGGGCTTTGTTGGCTTCTTTGTGCCCTGGTTCATCCCTAAAGGGCCTAACTGGGGAGTTGTCATCAC
CATGATGGTGACCTGTTCAGTTTGCTGCTCTCTTTTGGCTGATTGCAATTCTGGCCTAATGTAATCCTCTCTATGGACCA
TGCTTGAAAGATGAAACCACCTGGTATCTGAAGCATCACTGGCCT

Alignment

ORF - retro_cjac_1923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 85.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVFWGFVGFLVPWFIPKGPNRGVIITMLVTCSVCCY-LFWLIAILAQLNPLFGPQLKNETIWYLKYHWP
          MS.FWGFVGF.VPWFIPKGPN.G............C..LFWLIAILA..NPL.GP.LK.ET.WYLK.HWP
Retrocopy MSMFWGFVGFFVPWFIPKGPNWG-VVITMMVTCSVCC>LFWLIAILA*CNPLYGPCLKDETTWYLKHHWP

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
SRP051959_colon	0.62 RPM	17.73 RPM
SRP051959_heart	0.60 RPM	17.29 RPM
SRP051959_kidney	0.64 RPM	36.03 RPM
SRP051959_liver	0.89 RPM	26.86 RPM
SRP051959_lung	0.67 RPM	21.28 RPM
SRP051959_lymph_node	0.73 RPM	18.86 RPM
SRP051959_skeletal_muscle	0.50 RPM	9.74 RPM
SRP051959_spleen	0.90 RPM	32.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1923 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1923 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1923 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3240
Pan troglodytes	retro_ptro_2190
Gorilla gorilla	retro_ggor_2206
Pongo abelii	retro_pabe_2688

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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,