RetrogeneDB ID: retro_cpor_1468

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:16211943..16212556(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP1B3
• Ensembl ID: ENSCPOG00000003739
• Aliases: None
• Description: Sodium/potassium-transporting ATPase subunit beta-3 [Source:UniProtKB/Swiss-Prot;Acc:Q60489]

Sequence

>retro_cpor_1468
GAGAAGCCTTTGAATGAGAGCCTGGCCCGGTGGGAGCTCTTGTACAATCGGACCACCGGAAAATTCCTGGGGTGCACCCT
CAAGAGCTGGGGTTTGATCTTAGCTTCTACTTAGTGTTTTTTGGGTTCCTGGATGTACTCTTCTCATTCATAATTTGGGC
TATGTTTCAAACTCTGAATGATGAGGTTCCAAATACCATGACCAGATTCCTAGTCCAGGACTCATAGTTTTCCCAAAACT
AGTGACTGCATTGAAATATACATTTAGTGTATCTGATCCAAGTTCCTATGAAGGGTACATTAAAGACCTTTAGAAGTTTC
TAAAATCATATTCTTTAGATGAGCAGAGGAATCTCAACAACTTTGCTGATGGAGCGCTTTTTGAACAGAAGGGTCCAGTG
TTTGCTGCATGTCAAGTTTCTTCACTTCTTACTGGAAGTGTGCAGTGGTGCAAATGATCCTGACTTCAGCTATTTCCGAA
GACAACCTTGTATTCTTGTGAAAATGAACAGAATCATTGGATTAAAGCCTGCAGCACACCAAGGATAGACTGTATTTCAA
AGGATGAAAACACATCAATTGTATCCACTTATACTAATCATGGAGTCATAGAC

Alignment

ORF - retro_cpor_1468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.76 %
• Parental protein coverage: 73.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKSLNESLAQWKLFLYNPTTREFLGRTAKSWGLILL-FYLVFYGFLAALFTFTMWAMLQTLNDEIP-KYR
          .K.LNESLA.W.L.LYN.TT..FLG.T.KSWGLIL..FYLVF.GFL..LF.F..WAM.QTLNDE.P.KY.
Retrocopy EKPLNESLARWEL-LYNRTTGKFLGCTLKSWGLILA<FYLVFFGFLDVLFSFIIWAMFQTLNDEVP<KYH

Parental  DQIPSPGLMVFPKPVTALEYTFSVSDPSSYEGYIKDLKKFLKSYSLDEQKNLNKCTDGVLFEQTGPVYAA
          DQIPSPGL.VFPK.VTAL.YTFSVSDPSSYEGYIKDL.KFLKSYSLDEQ.NLN...DG.LFEQ.GPV.AA
Retrocopy DQIPSPGLIVFPKLVTALKYTFSVSDPSSYEGYIKDL*KFLKSYSLDEQRNLNNFADGALFEQKGPVFAA

Parental  CQ-FPDSLLEACSGTDDPDFGYSQGQPCVLVKMNRIIGLKPE-GSPRIDCISKDENTAMVSTYPNQGVID
          CQ.F...LLE.CSG..DPDF.Y...QPC.LVKMNRIIGLKP....PRIDCISKDENT..VSTY.N.GVID
Retrocopy CQ>FLHFLLEVCSGANDPDFSYFRRQPCILVKMNRIIGLKPA<STPRIDCISKDENTSIVSTYTNHGVID

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	46.76 RPM
SRP017611_kidney	0.00 RPM	84.48 RPM
SRP017611_liver	0.00 RPM	64.03 RPM
SRP040447_lung	0.00 RPM	81.44 RPM
SRP040447_skeletal_muscle	0.00 RPM	45.67 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1468 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1468 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 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014140	5 retrocopies	retro_btau_1136, retro_btau_1322, retro_btau_1743, retro_btau_318, retro_btau_920,
Choloepus hoffmanni	ENSCHOG00000007515	4 retrocopies	retro_chof_1000, retro_chof_1421, retro_chof_2393, retro_chof_2445,
Callithrix jacchus	ENSCJAG00000001981	1 retrocopy	retro_cjac_309,
Cavia porcellus	ENSCPOG00000003739	4 retrocopies	retro_cpor_1181, retro_cpor_1468 , retro_cpor_1506, retro_cpor_222,
Equus caballus	ENSECAG00000019885	2 retrocopies	retro_ecab_1084, retro_ecab_468,
Homo sapiens	ENSG00000069849	2 retrocopies	retro_hsap_1387, retro_hsap_2263,
Loxodonta africana	ENSLAFG00000010553	1 retrocopy	retro_lafr_815,
Mus musculus	ENSMUSG00000032412	2 retrocopies	retro_mmus_2174, retro_mmus_3427,
Nomascus leucogenys	ENSNLEG00000004663	1 retrocopy	retro_nleu_1286,
Otolemur garnettii	ENSOGAG00000008662	1 retrocopy	retro_ogar_2284,
Procavia capensis	ENSPCAG00000013927	1 retrocopy	retro_pcap_350,
Pongo abelii	ENSPPYG00000014169	1 retrocopy	retro_pabe_1953,
Pan troglodytes	ENSPTRG00000015476	2 retrocopies	retro_ptro_1603, retro_ptro_951,
Rattus norvegicus	ENSRNOG00000011501	2 retrocopies	retro_rnor_2571, retro_rnor_789,
Sus scrofa	ENSSSCG00000011676	3 retrocopies	retro_sscr_889, retro_sscr_945, retro_sscr_95,
Ictidomys tridecemlineatus	ENSSTOG00000013235	1 retrocopy	retro_itri_1663,
Tupaia belangeri	ENSTBEG00000001004	1 retrocopy	retro_tbel_3620,
Tarsius syrichta	ENSTSYG00000000222	1 retrocopy	retro_tsyr_330,
Tursiops truncatus	ENSTTRG00000012038	1 retrocopy	retro_ttru_333,