RetrogeneDB ID: retro_cpor_1063

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_42:7384093..7384619(-)
• Located in intron of: ENSCPOG00000006312

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA5
• Ensembl ID: ENSCPOG00000013670
• Aliases: None
• Description: Proteasome subunit alpha type [Source:UniProtKB/TrEMBL;Acc:H0VP94]

Sequence

>retro_cpor_1063
ATGTTTCAGGTGGAATATGCCATTGAGGCTATCAAGCTTGATTCTACAGCCATTGGGATCCAGACATTGAAAGGTGTATG
CCTAGCTGTGCAAAAAGAGATTTACTTCCCCACTCACGGAGCCCAGCAGCATTGAGAAAACAGTAGAGACTGATGCTCAT
ATAGGTTGTGCCATGAGTGGACTAACTGCTGATGCCAAGACTTTAATTAATAAGGCAGGAATGGAGACCCAGAACCAATG
GTTTACCTAAAATGAGACAATGACAGGGGAGCGTGTGACCCAGGCTGTGTTTCATCTGGCCCTACAGTTTGGAGAAGATG
ATGCAGATCCAGATGTCACACCTTGTCCCTTTGGAGTAGCACTGTTATTTGGAGGAGTTGATGAGAAGGGATCCCAGCTC
TTTCATAGGGACCCATCTGGGCCCTACGTACAGTGTGACACCTGAGAAATTGGCTCTGCTTCAGAAGGTGCCCAGAGCTC
CTTGCCAGAAGTTCACCACAAGTCAATGACACTGAAAGAAGTCATC

Alignment

ORF - retro_cpor_1063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.55 %
• Parental protein coverage: 72.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEK-RITSPLMEPSSIEKIVEIDAHIGCAMSGLIADAKTLI
          .FQVEYAIEAIKL.STAIGIQT..GVCLAV.K.R.TSPL.EPSSIEK.VE.DAHIGCAMSGL.ADAKTLI
Retrocopy MFQVEYAIEAIKLDSTAIGIQTLKGVCLAVQK>RFTSPLTEPSSIEKTVETDAHIGCAMSGLTADAKTLI

Parental  DKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPS
          .KA..ETQN.WFT.NETMT.E.VTQAV..LALQFGE.DADP.....PFGVALLFGGVDEKG.QLFH.DPS
Retrocopy NKAGMETQNQWFT*NETMTGERVTQAVFHLALQFGEDDADPDVTPCPFGVALLFGGVDEKGSQLFHRDPS

Parental  GTFVQCDARAIGSASEGAQSSLQEVYHKSMTLKEAI
          G..VQCD...IGSASEGAQSSL.EV.HKSMTLKE.I
Retrocopy GPYVQCDT*EIGSASEGAQSSLPEVHHKSMTLKEVI

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	0.23 RPM	24.39 RPM
SRP017611_kidney	0.10 RPM	49.20 RPM
SRP017611_liver	0.48 RPM	55.63 RPM
SRP040447_lung	0.10 RPM	42.67 RPM
SRP040447_skeletal_muscle	0.00 RPM	42.90 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1063 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1063 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013670	1 retrocopy	retro_cpor_1063 ,
Equus caballus	ENSECAG00000011835	1 retrocopy	retro_ecab_1106,
Echinops telfairi	ENSETEG00000012916	1 retrocopy	retro_etel_1053,
Mus musculus	ENSMUSG00000068749	1 retrocopy	retro_mmus_52,
Ochotona princeps	ENSOPRG00000008863	1 retrocopy	retro_opri_449,
Rattus norvegicus	ENSRNOG00000019868	2 retrocopies	retro_rnor_1230, retro_rnor_658,
Sus scrofa	ENSSSCG00000006830	2 retrocopies	retro_sscr_1156, retro_sscr_1194,