RetrogeneDB ID: retro_cpor_430

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_15:1208617..1209369(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS15
• Ensembl ID: ENSCPOG00000010877
• Aliases: None
• Description: None

Sequence

>retro_cpor_430
ATGTCGAGGGCCACATGGAAGGCACTGAGTTCATTTGGATTCTGGGCAGCAAATCAAGCTCCAGTCTTTGGTCTTCTGGG
AAGAGGGAGTACTAGGCTTCTCTCAGATCAATGGGGCCTGCAGCCTCAAAATCCACAGACTGCTCAAAGATTTTCCACTC
AGAAACCAGTCCAACTCAGACACATCAATGATCTACCCTATTTCATGCTCTTCAGAGGCCACCAAAACATCCCTGCAATC
GAGAAAGGTGATGACATTGTGTAAAGACTCTTTGGATATGGTCAACTGGAAAGAAATGCAAAAATTAAGCAAGAACATTT
TATGAACAAGTTCATGGCAAACCCTGAAGACACCAGATCGCTGGAGACTTGAATTGTTGCCTGGACCATTAAGATGTGCA
ATTATGAAGAATACATGCAGAAACAACCAAAGAACAAAGTCCACAAATGCTATCTACTGATGCACATTGACCAGAGAAAG
ATGTCCAAAAATCTCTGGAAGACCAACTATAATATATTTGAGAAGATATTCAGGGAGCTGAGATCAAGTACACCTTAGGA
GGACTCTACTACCAAAAAGCCCACCACCACTTCTTGGCCAAGAAGTTCATGTACATCTAAGTTTTCCAGGAGGTACAAAA
GCTGAAGAAGCAAAAACCAACCTTAATATCTGCAAAAGCAGCCCAGAGAGAAGATGGCTATCAGAACACAGAGGCTCCTT
TCAAAGTTTATAAAGAGGCACTTGAGGAAAAC

Alignment

ORF - retro_cpor_430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLKAAWRAVSLFGFRAATQAPVFGLPGRGRARLLSDQWGLQPQSLLQAACGYATQNPVQPCHDNDPPPST
          M..A.W.A.S.FGF.AA.QAPVFGL.GRG..RLLSDQWGLQPQ...Q.A....TQ.PVQ..H.ND.P...
Retrocopy MSRATWKALSSFGFWAANQAPVFGLLGRGSTRLLSDQWGLQPQN-PQTAQRFSTQKPVQLRHINDLPYFM

Parental  LLKDYQNVPGIEKVDDVVKRLLSLEMANRKEMLKVKQEQLMNKVMANPEDTRALETRIVALTVKIRNYEE
          L....QN.P.IEK.DD.V.RL.......R....K.KQE..MNK.MANPEDTR.LET.IVA.T.K..NYEE
Retrocopy LFRGHQNIPAIEKGDDIV*RLFGYGQLERN--AKIKQEHFMNKFMANPEDTRSLET*IVAWTIKMCNYEE

Parental  HMQKHRKDKAHKRYLLMSIDQRKKMLKNLRKTNYNIFERVCREL-GIEYTFPPLYYRKAHRRFLAKKALC
          .MQK..K.K.HK.YLLM.IDQR.KM.KNL.KTNYNIFE...REL..I.YT...LYY.KAH..FLAKK...
Retrocopy YMQKQPKNKVHKCYLLMHIDQR-KMSKNLWKTNYNIFEKIFREL<EIKYTLGGLYYQKAHHHFLAKKFMY

Parental  IQVFQEVQKLKKQKRAL-KAKAALKQDDHQNEEAHSKAYAEALEEN
          I.VFQEVQKLKKQK..L..AKAA...D..QN.EA..K.Y.EALEEN
Retrocopy I*VFQEVQKLKKQKPTLISAKAAQREDGYQNTEAPFKVYKEALEEN

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	0.40 RPM	35.66 RPM
SRP017611_kidney	0.42 RPM	46.59 RPM
SRP017611_liver	0.57 RPM	35.17 RPM
SRP040447_lung	0.08 RPM	19.04 RPM
SRP040447_skeletal_muscle	0.03 RPM	64.07 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_430 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_430 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 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001463	1 retrocopy	retro_amel_1564,
Canis familiaris	ENSCAFG00000030390	1 retrocopy	retro_cfam_1939,
Callithrix jacchus	ENSCJAG00000001852	3 retrocopies	retro_cjac_3095, retro_cjac_761, retro_cjac_859,
Cavia porcellus	ENSCPOG00000010877	1 retrocopy	retro_cpor_430 ,
Dipodomys ordii	ENSDORG00000007581	1 retrocopy	retro_dord_118,
Felis catus	ENSFCAG00000005265	1 retrocopy	retro_fcat_915,
Homo sapiens	ENSG00000116898	1 retrocopy	retro_hsap_1594,
Myotis lucifugus	ENSMLUG00000006475	1 retrocopy	retro_mluc_1945,
Monodelphis domestica	ENSMODG00000017813	1 retrocopy	retro_mdom_1094,
Mus musculus	ENSMUSG00000028861	1 retrocopy	retro_mmus_3447,
Nomascus leucogenys	ENSNLEG00000011467	1 retrocopy	retro_nleu_615,
Otolemur garnettii	ENSOGAG00000002656	2 retrocopies	retro_ogar_1327, retro_ogar_16,
Pongo abelii	ENSPPYG00000001537	1 retrocopy	retro_pabe_1310,
Pan troglodytes	ENSPTRG00000000541	1 retrocopy	retro_ptro_1071,
Sus scrofa	ENSSSCG00000026393	1 retrocopy	retro_sscr_1190,
Ictidomys tridecemlineatus	ENSSTOG00000000608	1 retrocopy	retro_itri_454,
Tupaia belangeri	ENSTBEG00000000958	4 retrocopies	retro_tbel_1633, retro_tbel_4438, retro_tbel_845, retro_tbel_882,
Tarsius syrichta	ENSTSYG00000008948	2 retrocopies	retro_tsyr_1612, retro_tsyr_372,
Tursiops truncatus	ENSTTRG00000002345	1 retrocopy	retro_ttru_1500,