RetrogeneDB ID: retro_cpor_1330

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:13998188..13999294(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSCPOG00000009552
• Aliases: None
• Description: None

Sequence

>retro_cpor_1330
AGCGTAGCCGCCAAGTACCGCCTGGCCTCGCTGTACGTGGGGGACCTGCACGCGGACGCCACGGAGGACCTGCTCTTCCG
CAAGTTCAGCGCGCGGGGCCCGTGCTGTCCATCCGCATCTGCAGGGACGTGGCCACGCGGCGCCCGCTGGGCTACGCCTA
CGTGAACTTCCTGCGGCCGGCGGACGCGCAGAAGGCACTGGACACCATGAACTTCGACGCGGTGGAGGGCAAACCCATCC
GCCTCATGTGGTCCCAGCGAGACGCCTGCTTGAGAAAATCGGGCGTCGGGAACGTGATCATCAAGAACCTGGACAGATCG
GTGGACAACAAGACCCTGTACGAGCACTTCTCGGGCTTCGGCAGGATCCTGTCCTCCAAGGTGATGAGCGATGACCAGGG
ATCCAAGGGCTACGCCTTCGTGCACTTCCAGAGCCAGAGCGCGGCGGACTGCGCCATCCAGGAGATGAACGGCAAGGTGA
TCCGGGACCGGCAGGTGCTGGTCGCCCCGTTCCGGAGCCGCAGGGACCGGGAAGCCGAGCTCAGAACCAGAACCAGTGAG
TTCACCAACGTGTACGTCAAGAACTTCGGCGAGGACATGGACGACGAGAGGCTGCAGGGTGTTTTCAGCAAATACGGCAG
AACCCTCAGCGTGAAGGTGATGACGGATTCCAGCGGAAAATCCAAAGGCTTCGGCTTCGTGAGCTTCGACAGCCACGAGG
CCGCCAAGAAGGCCGTGGAAGAAATGAACGGGAAGGACATCAACGGGCAGCTGGTGTTCGTGGGCAGAGCGCAGAAGAAA
GAAGAGCGCCAGGCCGAGCTGAAGCAGGTCTTCGAGGAGCTGAAGAGGGACGGCGCGCGCCGGTGCCAGGGCGTCAAACT
CTACATCAAGAACCTGGACGACACGGTGGACGATGACCGGCTGCGGAGGGCGTTTTCCTCATTTGGCTCCATCAGCAGGG
TCAAGGTCATGGAGGAAGAAGGGCAGCGCAAAGGCTTCGGCTTGGTGTGCTTCTCCTCCCCGGAGGAAGCTGCCAAAGCC
ATGACCCAGATGAACGGACGCGTCCTGGGCTCCAAACCCCTCAACATCGCCCTGGCCAAGCGCCAG

Alignment

ORF - retro_cpor_1330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.11 %
• Parental protein coverage: 55.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAASSYPMASLYVGDLHSDVTEAMLYEKFSP-AGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDT
          ..A..Y..ASLYVGDLH.D.TE..L..KFS..AGPVLSIR.CRD..TRR.LGYAYVNF..PADA..ALDT
Retrocopy SVAAKYRLASLYVGDLHADATEDLLFRKFSA<AGPVLSIRICRDVATRRPLGYAYVNFLRPADAQKALDT

Parental  MNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYA
          MNFD...GKPIR.MWSQRD..LRKSGVGNV.IKNLD.S.DNK.LY..FS.FG.ILS.KV..D..GSKGYA
Retrocopy MNFDAVEGKPIRLMWSQRDACLRKSGVGNVIIKNLDRSVDNKTLYEHFSGFGRILSSKVMSDDQGSKGYA

Parental  FVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDENLKELF
          FVHF..Q.AAD.AI..MNG....DR.V.V..F.SR..REAEL.....EFTNVY.KNFGE..DDE.L...F
Retrocopy FVHFQSQSAADCAIQEMNGKVIRDRQVLVAPFRSRRDREAELRTRTSEFTNVYVKNFGEDMDDERLQGVF

Parental  SQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEINGKIIFVGRAQKKVERQAELKRKFE
          S..G.TLSVKVM.D.SGKSKGFGFVS...HE.A.KAVEEMNGK.ING...FVGRAQKK.ERQAELK..FE
Retrocopy SKYGRTLSVKVMTDSSGKSKGFGFVSFDSHEAAKKAVEEMNGKDINGQLVFVGRAQKKEERQAELKQVFE

Parental  QLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVT
          .LK.....R.QGV.LYIKNLDDT.DD..LR..FS.FGSI...KVM.E.G..KGFG.VCFSSPEEA.KA.T
Retrocopy ELKRDGARRCQGVKLYIKNLDDTVDDDRLRRAFSSFGSISRVKVMEEEGQRKGFGLVCFSSPEEAAKAMT

Parental  EMNGRIVGSKPLYVALAQRK
          .MNGR..GSKPL..ALA.R.
Retrocopy QMNGRVLGSKPLNIALAKRQ

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	0.75 RPM	35.03 RPM
SRP017611_kidney	1.15 RPM	66.48 RPM
SRP017611_liver	0.44 RPM	33.04 RPM
SRP040447_lung	4.54 RPM	77.38 RPM
SRP040447_skeletal_muscle	0.81 RPM	440.71 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1330 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1330 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
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus	ENSCPOG00000002044	1 retrocopy	retro_cpor_1379,
Cavia porcellus	ENSCPOG00000009552	2 retrocopies	retro_cpor_1330 , retro_cpor_77,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Homo sapiens	ENSG00000090621	2 retrocopies	retro_hsap_109, retro_hsap_74,
Gorilla gorilla	ENSGGOG00000004002	3 retrocopies	retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Macaca mulatta	ENSMMUG00000007497	1 retrocopy	retro_mmul_178,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys	ENSNLEG00000011928	2 retrocopies	retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus	ENSOCUG00000000562	2 retrocopies	retro_ocun_153, retro_ocun_792,
Otolemur garnettii	ENSOGAG00000004067	1 retrocopy	retro_ogar_71,
Ochotona princeps	ENSOPRG00000011984	1 retrocopy	retro_opri_1133,
Pongo abelii	ENSPPYG00000001506	2 retrocopies	retro_pabe_190, retro_pabe_2563,
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,