RetrogeneDB ID: retro_ocun_1171

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:102932972..102933454(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5C1
• Ensembl ID: ENSOCUG00000004642
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 [Source:HGNC Symbol;Acc:833]

Sequence

>retro_ocun_1171
AGGGACATATTTTATAGGACTCATTCTGACCAGTTTCTCATGGTAGGCAAAGAGGTTGGGGAAAAACCCCCTACTTTTGG
AGATGTATCAGTCATTGCTCTTGAATTATTTAACTCTGCATGTGAATTTGATGAAGGGTCTATCATCTTTAACCAATTCA
AGTCTGTCATCTCCTATAAGATAGAAGAAAAGCCCATGTTTTCTCATAATACCATTGCAGGTGCTGAAAGCATGAGTAAT
CTTTGATGATGTTGCTGCTGATGTGCTGTGAAATTACCAAGAATACAATCAAGCCCATATCATCTACTACTCCCTGACGC
AGTCCACCACCAGTGAGCAGAGCGCGAGAATAACATCCTTGGCAATGCAGCACAAATGCTTCTGAGATGACTGACAGACT
AACTTTGACATTCAACTGTGCCACCCAAGCTGTCATCACAAAAGAGTTGATTGAAATTACCTCTGGTGCTACAGCTCTAG
AT

Alignment

ORF - retro_ocun_1171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.22 %
• Parental protein coverage: 54.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RGILHRTHSDQFLVTFKEVGRKPPTFGDASVIALELLNSGYEFDEGSIIFNRFKSVISYKTEEKPIFSLN
          R.I..RTHSDQFL...KEVG.KPPTFGD.SVIALEL.NS..EFDEGSIIFN.FKSVISYK.EEKP.FS.N
Retrocopy RDIFYRTHSDQFLMVGKEVGEKPPTFGDVSVIALELFNSACEFDEGSIIFNQFKSVISYKIEEKPMFSHN

Parental  TIASAESMS-IYDDVDADVLQNYQEYNLANIIYYSLKESTTSEQSARMTA-MDNASK-NASEMIDKLTLT
          TIA.AESMS.I.DDV.ADVL.NYQEYN.A.IIYYSL..STTSEQSAR.T....NA...NASEM.D.LTLT
Retrocopy TIAGAESMS>IFDDVAADVL*NYQEYNQAHIIYYSLTQSTTSEQSARITS<LGNAAQ<NASEMTDRLTLT

Parental  FNRTRQAVITKELIEIISGAAALD
          FN...QAVITKELIEI.SGA.ALD
Retrocopy FNCATQAVITKELIEITSGATALD

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
SRP017611_brain	0.00 RPM	190.12 RPM
SRP017611_kidney	0.00 RPM	432.89 RPM
SRP017611_liver	0.00 RPM	84.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1171 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1171 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005024	1 retrocopy	retro_cfam_1781,
Choloepus hoffmanni	ENSCHOG00000011229	3 retrocopies	retro_chof_102, retro_chof_297, retro_chof_673,
Callithrix jacchus	ENSCJAG00000020635	7 retrocopies	retro_cjac_1079, retro_cjac_1293, retro_cjac_1381, retro_cjac_1636, retro_cjac_2506, retro_cjac_4190, retro_cjac_526,
Cavia porcellus	ENSCPOG00000010523	2 retrocopies	retro_cpor_422, retro_cpor_984,
Echinops telfairi	ENSETEG00000010549	1 retrocopy	retro_etel_1406,
Felis catus	ENSFCAG00000000196	1 retrocopy	retro_fcat_818,
Homo sapiens	ENSG00000165629	1 retrocopy	retro_hsap_1415,
Gorilla gorilla	ENSGGOG00000009719	1 retrocopy	retro_ggor_1094,
Macaca mulatta	ENSMMUG00000009207	1 retrocopy	retro_mmul_2254,
Monodelphis domestica	ENSMODG00000016720	1 retrocopy	retro_mdom_1287,
Mus musculus	ENSMUSG00000025781	4 retrocopies	retro_mmus_1122, retro_mmus_2008, retro_mmus_3451, retro_mmus_3644,
Nomascus leucogenys	ENSNLEG00000011917	1 retrocopy	retro_nleu_1836,
Oryctolagus cuniculus	ENSOCUG00000004642	2 retrocopies	retro_ocun_1171 , retro_ocun_363,
Otolemur garnettii	ENSOGAG00000015242	2 retrocopies	retro_ogar_1099, retro_ogar_2738,
Procavia capensis	ENSPCAG00000004971	1 retrocopy	retro_pcap_99,
Pongo abelii	ENSPPYG00000002076	1 retrocopy	retro_pabe_1170,
Pan troglodytes	ENSPTRG00000002277	1 retrocopy	retro_ptro_968,
Pteropus vampyrus	ENSPVAG00000006512	3 retrocopies	retro_pvam_1466, retro_pvam_51, retro_pvam_530,
Ictidomys tridecemlineatus	ENSSTOG00000026133	1 retrocopy	retro_itri_665,
Tupaia belangeri	ENSTBEG00000011530	4 retrocopies	retro_tbel_1763, retro_tbel_2023, retro_tbel_4384, retro_tbel_4406,
Tarsius syrichta	ENSTSYG00000003035	4 retrocopies	retro_tsyr_1268, retro_tsyr_1988, retro_tsyr_465, retro_tsyr_506,