RetrogeneDB ID: retro_cpor_109

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_169:1449255..1450209(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000026239
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000000948
• Aliases: None
• Description: None

Sequence

>retro_cpor_109
CGTGATGGCTCCAACAGTCCCCACCATGCAGTATGCAAGTGTTTCCAGCAAGGGTACTGTGTTTGTGGAGACCGCTGCAG
ATGCGAGCACAGCAAGCCCCTGAAACAGGACGACGCAGCTGCTGCAGATGTAACCGTAAGACCGTCCCTCGTTGCTGCCT
CAAGTCTTTTCCCCATTGTTGCTGGACCACTTGTGGAGAGGAGAATGGGCAAAGCTGAGTCCAAAACTGTGAACTTCCCA
GCCATAGGCCCAGGTTCCAAGGACTGGGCAAATGCTGTTGAGTTTGTGCCTGGGCAGCCCTACCATGGTCGCATCGCCCC
TGCCTGCTCAGAAGCCTCTGCACAGGAATTGGTGCCCAAGGCCGAGTCGCAAAAGGAGCCCGCTGCGGTGGAGGCCAAAC
AGCAGGTCTGCCCCTACGCTGCTGTGGGAGAATGCTGCAACAAGGAGAACTGCATGTATCTGCATGGCGATGCCTGTGAC
ATGTGTGGGCTACAGGTCCTGCACCCGACAGATCCAGCCCAGAGGTCCCAGCACATAAAGTCTTGCATTGAGGCCCACGA
GAAGGATATGGAGCTGTCCTTTGCTGTGCAGCGCAGCAAAGACATGATGTGTGACATCTGCATGGAGGTGGTGTATGAGA
AAGCCAGACCCAGCGAGCGTCGCTTTGGTATCCTCTCCAACTGCAATCACACCTACTGTCTCAAGTGTATCCGCGAGTGG
AGGAGTGCTAAGCAGTTTGACAGCAAGATCATAAAGTCCTGCCCTGAATGCCGGATCACATCTAACTTTGTCATTCCAAG
TGAGTACTGGGTGGAAGAGAAAGAAGAAAAGCAGAAACTCATTCGGAAATACCAGGAGGCAATGAGCAACAAGGTATGCA
GGTATTTTGATGAAGGCCGTGGGAGCTGCCCATTTGGAAGAAACTGTTTTTATAAGCACGCATACCCCGGGGGA

Alignment

ORF - retro_cpor_109 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.5 %
• Parental protein coverage: 74.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLSDSPYGVVCKYFQRGYCVYGDRCRYEHSKPLKQEEAAATDLTTKPSLAAAPSLSS-GAGQLVEMNTDE
          D.S.SP...VCK.FQ.GYCV.GDRCR.EHSKPLKQ..AAA.D.T..PSL.AA.SL....AG.LVE.....
Retrocopy DGSNSPHHAVCKCFQQGYCVCGDRCRCEHSKPLKQDDAAAADVTVRPSLVAASSLFPIVAGPLVERRMGK

Parental  AESRNANLPAVGAGSEDWVNAIEFVPGQPYCGRTAPACTETPVQGPVPKAESEKEPAAVETKKQLCPYAA
          AES...N.PA.G.GS.DW.NA.EFVPGQPY.GR.APAC.E...Q..VPKAES.KEPAAVE.K.Q.CPYAA
Retrocopy AESKTVNFPAIGPGSKDWANAVEFVPGQPYHGRIAPACSEASAQELVPKAESQKEPAAVEAKQQVCPYAA

Parental  VGECRYGENCVYLHGDACDMCGLQVLHPVDTAQRSQHIKSCIEAHEKDMELSFAVQRSKDMVCGICMEVV
          VGEC...ENC.YLHGDACDMCGLQVLHP.D.AQRSQHIKSCIEAHEKDMELSFAVQRSKDM.C.ICMEVV
Retrocopy VGECCNKENCMYLHGDACDMCGLQVLHPTDPAQRSQHIKSCIEAHEKDMELSFAVQRSKDMMCDICMEVV

Parental  YEKANPSERRFGILSNCSHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVIPSEYWVEEKEEKQKLI
          YEKA.PSERRFGILSNC.HTYCLKCIR.WRSAKQF.SKIIKSCPECRITSNFVIPSEYWVEEKEEKQKLI
Retrocopy YEKARPSERRFGILSNCNHTYCLKCIREWRSAKQFDSKIIKSCPECRITSNFVIPSEYWVEEKEEKQKLI

Parental  QKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAYPDG
          .KY.EAMSNK.CRYFDEGRGSCPFG.NCFYKHAYP.G
Retrocopy RKYQEAMSNKVCRYFDEGRGSCPFGRNCFYKHAYPGG

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	3.22 RPM	34.97 RPM
SRP017611_kidney	1.15 RPM	49.41 RPM
SRP017611_liver	0.87 RPM	42.40 RPM
SRP040447_lung	2.95 RPM	64.04 RPM
SRP040447_skeletal_muscle	0.73 RPM	33.49 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_109 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_109 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 24 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Choloepus hoffmanni	ENSCHOG00000011015	3 retrocopies	retro_chof_173, retro_chof_2357, retro_chof_89,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109 ,
Dasypus novemcinctus	ENSDNOG00000019564	2 retrocopies	retro_dnov_1011, retro_dnov_388,
Erinaceus europaeus	ENSEEUG00000001133	1 retrocopy	retro_eeur_643,
Felis catus	ENSFCAG00000024942	1 retrocopy	retro_fcat_67,
Homo sapiens	ENSG00000133606	4 retrocopies	retro_hsap_1140, retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Macropus eugenii	ENSMEUG00000007399	1 retrocopy	retro_meug_1659,
Microcebus murinus	ENSMICG00000002114	1 retrocopy	retro_mmur_1184,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus	ENSMUSG00000029922	1 retrocopy	retro_mmus_2663,
Nomascus leucogenys	ENSNLEG00000001921	4 retrocopies	retro_nleu_1027, retro_nleu_2167, retro_nleu_33, retro_nleu_939,
Otolemur garnettii	ENSOGAG00000009877	2 retrocopies	retro_ogar_3468, retro_ogar_424,
Ochotona princeps	ENSOPRG00000010353	1 retrocopy	retro_opri_1073,
Procavia capensis	ENSPCAG00000014683	1 retrocopy	retro_pcap_19,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes	ENSPTRG00000019766	5 retrocopies	retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa	ENSSSCG00000016498	2 retrocopies	retro_sscr_43, retro_sscr_637,
Tupaia belangeri	ENSTBEG00000004564	2 retrocopies	retro_tbel_1410, retro_tbel_71,
Tarsius syrichta	ENSTSYG00000009996	3 retrocopies	retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus	ENSTTRG00000009528	2 retrocopies	retro_ttru_1064, retro_ttru_1128,