RetrogeneDB ID: retro_cpor_150

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:21729331..21730024(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000026078
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSCPOG00000007279
• Aliases: None
• Description: None

Sequence

>retro_cpor_150
CAGCAGCAAGCCAGTGACCCAGAGAAGGGGGCCGAGTGCCTCCAGAGGGAAGTAGAGGGAGAAAGCCGGGCTTGGGAACA
GGCTGAGGCAGAAGTGGCCTCCTTAAACGGCAGGATCCAGCTCATTGAAGAGAAGCTGGACCATGCACAGGAGCGCCTGG
CCCCTGCCCTGCAAAAGCTGGAGGAAGCTGAGAAAGCCTCCGAGGAGAGTGAGAGGGGAACGATCGTTAGTGAAAACCCA
ACTGTAAAAGATAAAGAAAAGATGGAACTCCAGGAATCTGACTTCAGTGGGTTAAACACACTGCAGAAGAGACAGACAGG
AAATGTGAGGAGTTGGTTAGTAAGTTGACATTTATTGAAGTTGATTTGGAACACACAGAGGACAGCGCTGAGCTGGCAGA
GTCCCATTGCCAGGAGAAGGATGAGCGGATCAGACTGATGGACCAGAACCTGCAGGATCTGCGCGCTGCTGAAGATAAGC
ACTCTCAAAAAGAAAACAAATATAAGGAAGAGATAAAGATGCTTACTGATAAACTCAAGGAGGCGGAGACCCACGCTGAG
CTTGCTGAGAGATCAGTTGCCAACCTGGAAAAGACAACCGATGGACTTGGAAGAGAAGCTGAAATGCACCACAGAGGAGC
AGCTCTGTGTGCGAAGGATGCTGGGCCAGGCCCTGCCCTATCTGCAGGAGATG

Alignment

ORF - retro_cpor_150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.1 %
• Parental protein coverage: 93.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADES
          QQQA.D.E..AE.LQREVEGE.RA.EQAEAEVASLN.RIQL.EE.LD.AQERLA.ALQKLEEAEKA..ES
Retrocopy QQQASDPEKGAECLQREVEGESRAWEQAEAEVASLNGRIQLIEEKLDHAQERLAPALQKLEEAEKASEES

Parental  ERGMKVIENRALKDEEKMELQE-IQLKEAKHIAEEADRKYEEVARKLVIIEGDLERTEERAELAESRCRE
          ERG..V.EN...KD.EKMELQE.I.L...KH.AEE.DRK.EE...KL..IE.DLE.TE..AELAES.C.E
Retrocopy ERGTIVSENPTVKDKEKMELQE<I*LQWVKHTAEETDRKCEELVSKLTFIEVDLEHTEDSAELAESHCQE

Parental  MDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSVAKLEKTID-DLEDKLK
          .DE.IRLMDQNL..L.AAE.K.SQKE.KY.EEIK.LTDKLKEAET.AE.AERSVA.LEKT.D.DLE.KLK
Retrocopy KDERIRLMDQNLQDLRAAEDKHSQKENKYKEEIKMLTDKLKEAETHAELAERSVANLEKTTD>DLEEKLK

Parental  CTKEEHLCTQRMLDQTLLDLNEM
          CT.EE.LC..RML.Q.L..L.EM
Retrocopy CTTEEQLCVRRMLGQALPYLQEM

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	0.06 RPM	71.38 RPM
SRP017611_kidney	0.00 RPM	37.06 RPM
SRP017611_liver	0.00 RPM	28.86 RPM
SRP040447_lung	0.00 RPM	112.31 RPM
SRP040447_skeletal_muscle	0.00 RPM	2466.71 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_150 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_150 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 13 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011877	2 retrocopies	retro_amel_1017, retro_amel_1212,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210, retro_btau_933,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Cavia porcellus	ENSCPOG00000007279	1 retrocopy	retro_cpor_150 ,
Dasypus novemcinctus	ENSDNOG00000019156	7 retrocopies	retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus	ENSECAG00000010942	1 retrocopy	retro_ecab_390,
Felis catus	ENSFCAG00000012596	1 retrocopy	retro_fcat_1441,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Myotis lucifugus	ENSMLUG00000013331	1 retrocopy	retro_mluc_1038,
Macaca mulatta	ENSMMUG00000010805	10 retrocopies	retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829, retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furo	ENSMPUG00000007875	1 retrocopy	retro_mputfur_604,
Mus musculus	ENSMUSG00000027940	1 retrocopy	retro_mmus_21,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8,