RetrogeneDB ID: retro_cpor_545

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_19:16489876..16490628(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDK1
• Ensembl ID: ENSCPOG00000008434
• Aliases: None
• Description: None

Sequence

>retro_cpor_545
CACAATGATGCCATTCCCATCATGGCCCAGGATGTGACTGAGAACAAAGAGAGCTTTGGGGTGGCTCCTGTCACCATACA
GAATGTTCAGTGCTTTTTGAGTTGATTCTATATGGGTTGTATTGCAACTAGAATGTTACTCACTCAGCACTCTTCACAGT
CTGGGGGAAAAGGAAGTGCATCTCATCAAAAACACAGTGGCAGCATAAATCCAAAGTATGATGTAGCCGGAGCTGTTAAA
GATGGCTATGGGAATGCTAGGCGTCTGTGTGATCTGTATCACACTAACTCTCCTGAACTAGAACTTGAACTGATGCAAAA
TCACCAGGACAACCAGGACAAACGGATGATATGCCTTTCCATCTCTGTCTCATGGTGTTTGAACTTTTCAAGAGCACATG
AGAGCAACTATGGAACGCCAAGCAGACAAAGGTGTTGACCTCCCTGTTCAAGTTCATTCAACATTGGGTAACGAGGATTT
GACGTGAAGAAGAGAGACCGGGAGGTGGCAGCCCTTTGAGGAAGAGTTAACAGACTCTTCAACTACGCACATTCAACTGC
GCCATGGCCATGTGTGGAGACTTCCCGAGTACACCCCTGGCTAGTTTTGGTTATAGGTTGCCCGAATGGCGTCTGTATGC
ACAGTACTTCCAAAGGGACCTGAAGCTGTATTTCTTGGAGGAGTACCACATGGATGCTATTATTTCCATAGAGGCTCTGT
TAACAGAAGCAATTGAGAGACTCTCAGGGTAT

Alignment

ORF - retro_cpor_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.73 %
• Parental protein coverage: 58.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  HNDVIPTMAQGVIEYKESFGVDPVTSQNVQYFLDRFYMSRISIRMLLNQHSLLFGGKGSPSHRKHIGSIN
          HND.IP.MAQ.V.E.KESFGV.PVT.QNVQ.FL..FYM..I..RMLL.QHS...GGKGS.SH.KH.GSIN
Retrocopy HNDAIPIMAQDVTENKESFGVAPVTIQNVQCFLS*FYMGCIATRMLLTQHSSQSGGKGSASHQKHSGSIN

Parental  PNCDVVEVIKDGYENARRLCDLYYINSPELELEEL-NAKSPGQPIQVVYVPSHLYHMVFELFKNA-MRAT
          P..DV....KDGY.NARRLCDLY..NSPELEL.EL..AKSPGQP.Q....P.HL..MVFELFK...MRAT
Retrocopy PKYDVAGAVKDGYGNARRLCDLYHTNSPELEL-EL<DAKSPGQPGQTDDMPFHLCLMVFELFKST<MRAT

Parental  MEHHADKGVYPPIQVHVTLGNEDLT-VKMSDR-GGGVPLRK-IDRLFNYMYSTAPRPRVETSR-AAPLAG
          ME..ADKGV..P.QVH.TLGNEDLT.VK..DR.GGG.PLRK...RLFNY..STAP.P.VETSR...PLA.
Retrocopy MERQADKGVDLPVQVHSTLGNEDLT<VKKRDR<GGGSPLRK>VNRLFNYAHSTAPWPCVETSR<STPLAS

Parental  FGYGLPISRLYAQYFQGDLKLYSLEGYGTDAVIYIKALSTESIERLPVY
          FGY.LP..RLYAQYFQ.DLKLY.LE.Y..DA.I.I.AL.TE.IERL..Y
Retrocopy FGYRLPEWRLYAQYFQRDLKLYFLEEYHMDAIISIEALLTEAIERLSGY

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	30.08 RPM
SRP017611_kidney	0.00 RPM	25.54 RPM
SRP017611_liver	0.00 RPM	18.54 RPM
SRP040447_lung	0.00 RPM	16.02 RPM
SRP040447_skeletal_muscle	0.00 RPM	15.80 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_545 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_545 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007507	1 retrocopy	retro_cjac_4090,
Cavia porcellus	ENSCPOG00000008434	1 retrocopy	retro_cpor_545 ,
Macaca mulatta	ENSMMUG00000022553	1 retrocopy	retro_mmul_2511,
Monodelphis domestica	ENSMODG00000009035	2 retrocopies	retro_mdom_107, retro_mdom_1447,
Otolemur garnettii	ENSOGAG00000014761	1 retrocopy	retro_ogar_509,