RetrogeneDB ID: retro_ptro_968

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:52937848..52938741(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5C1
• Ensembl ID: ENSPTRG00000002277
• Aliases: None
• Description: ATP synthase subunit gamma [Source:UniProtKB/TrEMBL;Acc:H2R2Y8]

Sequence

>retro_ptro_968
ATGTTCTCTCATGCGGGCATCACTGGGCTGTTGGCCTGGACCTTGCAGCCACAATGGATTCAAGTTCGAAATACAGCAAC
TTTGAACGATGTTACCAAGCGACTAAAGTCCATCAAAAACATCCAGAAAATTACCAAGTCTATGCAGATGGTAGCAGCAG
CAAAATACGCCCGAGCTGAGAGAGAGCTGAAACCAGCTTGAATATATGGATTGGGATCTTTGGCTCTGGAGAAAAAGCTG
GTATCAAGGTGCCTGAAGACAACAAGAAACACCTCCTTATTGGTGTGTCCTCAGATCGAGGACTGTGTGGCGCTATTCAT
TCCTCCATTGCTAAACAGATGAAAAGCGAGGTTGCTACACTAACAGCAGCTGGGAAAGAAGTTATGCTTGTTGGAATTGG
TGACAAAATCAGGGGCATACTTTATAGGATGCATTCTGACCAGTTTCTGGTGGCATTAAAAGAACTGAGAAGAAAGCCCC
CTGCTTTTGGAAATGTGTCAGTCATTGCCCTTGAATTACTAAATTCTGGATATGAATTTGATGAAGGCTCCATCATCTTT
AATCAGTTCAAGTCTGTCATCTCGTATAAGACTGAAGAAAAGCCCATCTTTTCCCTTAATACCATTGCAAGTGCCGAGAG
CATGAGTATCTACTATAATATTGATGCTGATGTGCTGCAAAATTACCAGGAATACAATCTGGCCAACAGCATCTACTACT
CTCTGAAGGAGTCCACCACTAGTGAGCAGAGTGCCAGGATGACAGCCATGGACAACACCAGCAAGAGTGCCTCTGAGATG
ATTGACAAATTGACATTGACATTCAACTGTACCCGCCAAGCTGTCATCACAAAAGAGTTGACTGAAATTATCTTTGGTGC
TGTAGCTCTGGAT

Alignment

ORF - retro_ptro_968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFSRAGVAGLSAWTLQPQWIQVRNMATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARIYG
          MFS.AG..GL.AWTLQPQWIQVRN.ATL.D.T.RLKSIKNIQKITKSM.MVAAAKYARAERELKPA.IYG
Retrocopy MFSHAGITGLLAWTLQPQWIQVRNTATLNDVTKRLKSIKNIQKITKSMQMVAAAKYARAERELKPA*IYG

Parental  LGSLALY-EKADIKGPEDKKKHLLIGVSSDRGLCGAIHSSIAKQMKSEVATLTAAGKEVMLVGIGDKIRG
          LGSLAL..EKA.IK.PED.KKHLLIGVSSDRGLCGAIHSSIAKQMKSEVATLTAAGKEVMLVGIGDKIRG
Retrocopy LGSLALE<EKAGIKVPEDNKKHLLIGVSSDRGLCGAIHSSIAKQMKSEVATLTAAGKEVMLVGIGDKIRG

Parental  ILYRTHSDQFLVAFKEVGRKPPTFGDASVIALELLNSGYEFDEGSIIFNKFRSVISYKTEEKPIFSLNTV
          ILYR.HSDQFLVA.KE..RKPP.FG..SVIALELLNSGYEFDEGSIIFN.F.SVISYKTEEKPIFSLNT.
Retrocopy ILYRMHSDQFLVALKELRRKPPAFGNVSVIALELLNSGYEFDEGSIIFNQFKSVISYKTEEKPIFSLNTI

Parental  ASADSMSIYDDIDADVLQNYQEYNLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTR
          ASA.SMSIY..IDADVLQNYQEYNLAN.IYYSLKESTTSEQSARMTAMDN.SK.ASEMIDKLTLTFN.TR
Retrocopy ASAESMSIYYNIDADVLQNYQEYNLANSIYYSLKESTTSEQSARMTAMDNTSKSASEMIDKLTLTFNCTR

Parental  QAVITKELIEIISGAAALD
          QAVITKEL.EII.GA.ALD
Retrocopy QAVITKELTEIIFGAVALD

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	77.77 RPM
SRP007412_cerebellum	0.07 RPM	72.59 RPM
SRP007412_heart	0.17 RPM	296.85 RPM
SRP007412_kidney	0.05 RPM	212.82 RPM
SRP007412_liver	0.00 RPM	85.44 RPM
SRP007412_testis	0.00 RPM	45.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_968 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_968 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1415
Gorilla gorilla	retro_ggor_1094
Pongo abelii	retro_pabe_1170

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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,