RetrogeneDB ID: retro_cpor_1516

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_91:3556761..3557318(-)
• Located in intron of: ENSCPOG00000012322

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000004251
• Aliases: None
• Description: None

Sequence

>retro_cpor_1516
CCTAAGAAGTCCAAACAGCTGTGGAAGCTCTTCATTGGAGGGCTGAACTTTGACAAAACTGATGAGAGTCTAAGAAGCCA
TTTTAAGCAACGGGGAACAATCACAGAGTGTGTGGTAACGAGAGATCCAAACACCAGGCATTCCAAAGACTTGGGTTTGT
CACTTATGCCACTGTGGAGGAGGTGGATGAGCCATGAATGCAAGGCCACACAAAGTGCATGGAAGAGTTGCGGAACCAAA
GAGAGCAGTCTCAAAAGAAGATTTTTCAAAGACCAGGTGCCTGCTTAATTGTGAAGATCTTTGCTGGTGGCATTAAAGAA
GATACTGATGAACATCACCTATGAGATTATTTTGAACAGAATGGAAAAACTGAAGTGCTTGAAATCATGACTAAGGCAGT
TGAAAGAAGTGGGGCTTTGCTTCTGTAACCTTTGATGACCATGATTCCATGGCTGACTGTCATTCAGAAATACCATACTG
TGAACGGCGACAACTGTGAAGCAAAGAAAGCTCTGTCGAAGTAGGAGATAGCTAGTGCTTAATTTAGCCAAAGAGGT

Alignment

ORF - retro_cpor_1516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.55 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFG-FVTYSCVEEVDA-AMCA
          PK...QL.KLFIGGL.F..TD.SLR.HF...GT.T.CVV.RDP.T..S...G.FVTY..VEEVD..AM.A
Retrocopy PKKSKQLWKLFIGGLNFDKTDESLRSHFKQRGTITECVVTRDPNTRHSKDLG<FVTYATVEEVDE<AMNA

Parental  RPHKVDGRVVEPKRAVSREDSVK-PGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSG
          RPHKV.GRV.EPKRAVS.ED..K.PGA.L.VK.IF.GGIKEDT.E..L.DYFE..GK....EV.E.....
Retrocopy RPHKVHGRVAEPKRAVSKEDFSK>PGACLIVK-IFAGGIKEDTDEHHL*DYFEQNGKT---EVLEIMTKA

Parental  KKRGFAFVTFDDHDTVDKIVVVQKYHTINGHNCEVKKALSKQEMQSA-GSQRG
          ..R..A..............V.QKYHT.NG.NCE.KKALSK.E..SA..SQRG
Retrocopy VERSGALLL*PLMTMIPWLTVIQKYHTVNGDNCEAKKALSK*EIASA*FSQRG

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	0.00 RPM	46.47 RPM
SRP017611_kidney	0.00 RPM	60.20 RPM
SRP017611_liver	0.00 RPM	37.52 RPM
SRP040447_lung	0.03 RPM	88.50 RPM
SRP040447_skeletal_muscle	0.00 RPM	28.66 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1516 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1516 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 16 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516 , retro_cpor_1543, retro_cpor_65,
Cavia porcellus	ENSCPOG00000015619	5 retrocopies	retro_cpor_1110, retro_cpor_1318, retro_cpor_264, retro_cpor_274, retro_cpor_567,
Cavia porcellus	ENSCPOG00000020972	1 retrocopy	retro_cpor_1078,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Mustela putorius furo	ENSMPUG00000014103	6 retrocopies	retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,