RetrogeneDB ID: retro_cpor_984

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_38:13921332..13922159(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5C1
• Ensembl ID: ENSCPOG00000010523
• Aliases: None
• Description: ATP synthase gamma chain [Source:UniProtKB/TrEMBL;Acc:H0VH31]

Sequence

>retro_cpor_984
ATCCAAATCAGAAATATGGCAGCTTTGCAAGACATTACCCAGCAACTAAAGTCAATCAAAAATATCCAGAAAATACCAAG
TCTATGAAAATGGTAGCAGCAGCAAAATATGCTCGAGCTGAGAGGGAGCTGAAACCGGCTGGGATATATGGAATAAGATC
TTTAGCTCTGCATGAAAAAGCTGATATTAAGGTACCTGAAGACAAGAAAAAACACCTTCTCATTGGTGTGTCCTCAGATC
AAGAGCTTTGTGGTGCTACTTATTCCTAAATCGCTAAACCATGAAAAATGAGCTGGCCACAAACAGCAGCTGGAAAAGAG
GTCAGGATTGTTGGAACTGGTGATAAAATCAGGGGCATATTTTCCAGGACCCATTCTGACCAGTTTCTGGTGATGTTCAA
GGCTGTAGGGAGAAAGCCCCCTTTTGAAGATGCATCCATTATTGCTCTGGAATTACTAAATTCTGGATATGCGTTTGATG
AAGACTCTGTCATCTTTAATCAGTTTAGGTCTGTTATCTCCTACAAGACAGAAGAAAAGCCCATCTTTTCTCTTGATACC
ATTGCAAGTGCTGAGAGCATGAACATCTATGATGATATTGATTCCAGTGTGCTGCAGAATTACCAAGAGTGTAGTCTGGT
CAACATCGTCTGCTACTCCCTGAAGGAATCTACCATCAGTGAGCAGAGTGCCAGGATGACAGGGATGGACGGTGTTAGTA
AGAACGCTTCTGAGATGATTGATAAATTGACTCTGACATACGGATGTACCCACCAAGCCATCATCACCAAAGAGTTGAAG
GAGATCGTCTCCAAAGCAGGAGCTCTG

Alignment

ORF - retro_cpor_984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQVRNMATLKDITRRLKSIKNIQKI-TKSMKMVAAAKYARAERELKPARIYGIGSLALYEKADIKVPEDK
          IQ.RNMA.L.DIT..LKSIKNIQKI.TKSMKMVAAAKYARAERELKPA.IYGI.SLAL.EKADIKVPEDK
Retrocopy IQIRNMAALQDITQQLKSIKNIQKI<TKSMKMVAAAKYARAERELKPAGIYGIRSLALHEKADIKVPEDK

Parental  KKHLLIGVSSDRGLCGAIHASVAKQIKNEVATLTAAGKEVMIVGIGDKIRGILSRTHSDQFLVTFKDVGR
          KKHLLIGVSSD..LCGA.....AK..K......TAAGKEV.IVG.GDKIRGI.SRTHSDQFLV.FK.VGR
Retrocopy KKHLLIGVSSDQELCGATYS*IAKP*KMSWPQ-TAAGKEVRIVGTGDKIRGIFSRTHSDQFLVMFKAVGR

Parental  KPPTFGDASVIALELLNSGYEFDDGSIIFNRFRSVISYKTEEKPIFSLNTIASAESMSIYDDIDADVLQN
          KPP.F.DAS.IALELLNSGY.FD..S.IFN.FRSVISYKTEEKPIFSL.TIASAESM.IYDDID..VLQN
Retrocopy KPP-FEDASIIALELLNSGYAFDEDSVIFNQFRSVISYKTEEKPIFSLDTIASAESMNIYDDIDSSVLQN

Parental  YQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKELIEIISGAAAL
          YQE.SL.NI..YSLKEST.SEQSARMT.MD..SKNASEMIDKLTLT...T.QA.ITKEL.EI.S.A.AL
Retrocopy YQECSLVNIVCYSLKESTISEQSARMTGMDGVSKNASEMIDKLTLTYGCTHQAIITKELKEIVSKAGAL

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	0.06 RPM	70.75 RPM
SRP017611_kidney	0.52 RPM	192.10 RPM
SRP017611_liver	0.00 RPM	168.32 RPM
SRP040447_lung	0.03 RPM	56.75 RPM
SRP040447_skeletal_muscle	0.00 RPM	232.13 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_984 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_984 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,