RetrogeneDB ID: retro_cpor_161

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:72945141..72945647(-)
• Located in intron of: ENSCPOG00000002251

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHYH
• Ensembl ID: ENSCPOG00000007582
• Aliases: None
• Description: None

Sequence

>retro_cpor_161
GGCAGTAAGACAGCAGGTCATCCTGTGCACCAGGATCTGCACTATTTACCTTTTCGACCCATTGATCACATTGTTGGTAT
TTGGACCACAGTGGAGCACACTGCCCAGATAAAAAGTTGTTTGTTCGTGCCTCCAGGCACCCACAAAAGTTCTGTGAAGC
CACATGGTTACCCCAGTGGGAGGGTGGAGTGAATCTAATGTTCCACAGGATCCAGGACTATGAACAGGACAATACCTATA
TACATCTCATAATGGACAAGGGAGACACTGTTTTCTTTCATCCTTTGGTTGTCCATGGATCTGGCTGGAACAGAACTCAA
GGTTTTAGGAAAGTAATTTTCTGCCATTATGCCAGTGCCAGTTGCCACATCACTGTGAAGGGCACCAATCAAGACATTGA
GAAAGAAGTGATAAAAATAGCAAACAAATTTGGCACAACTAATGTCAGCTTGAAGGATATTTGGAAGTTTCGAGCCTAGC
TTGTGACAGGAGAACAAATTAACCTT

Alignment

ORF - retro_cpor_161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.19 %
• Parental protein coverage: 50.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKKTSRHPMHQDLHYFSFRPSDRIVAAWTAMEHIDRSNGCLVVLPGSHKSSLKPHGYP-EWEGGVNIVFH
          G.KT..HP.HQDLHY..FRP.D.IV..WT..EH......CL.V.PG.HKSS.KPHGYP..WEGGVN..FH
Retrocopy GSKTAGHPVHQDLHYLPFRPIDHIVGIWTTVEHTAQIKSCLFVPPGTHKSSVKPHGYP<QWEGGVNLMFH

Parental  GIQDYQKDNARVHLIMDKGDTVFFHPLLIHGSGRNRTQGFRKAISCHFASSSCHYIDVKGTNQENVEKEV
          .IQDY..DN...HLIMDKGDTVFFHPL..HGSG.NRTQGFRK.I.CH.AS.SCH.I.VKGTNQ...EKEV
Retrocopy RIQDYEQDNTYIHLIMDKGDTVFFHPLVVHGSGWNRTQGFRKVIFCHYASASCH-ITVKGTNQD-IEKEV

Parental  MKIFNKMGLTDVSLKDFWKFRARLVKGERINL
          .KI.NK.G.T.VSLKD.WKFRA.LV.GE.INL
Retrocopy IKIANKFGTTNVSLKDIWKFRA*LVTGEQINL

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	1.44 RPM	24.10 RPM
SRP017611_kidney	0.42 RPM	840.54 RPM
SRP017611_liver	0.17 RPM	2170.33 RPM
SRP040447_lung	0.68 RPM	31.37 RPM
SRP040447_skeletal_muscle	0.37 RPM	81.34 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_161 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_161 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002160	1 retrocopy	retro_chof_334,
Cavia porcellus	ENSCPOG00000007582	1 retrocopy	retro_cpor_161 ,
Rattus norvegicus	ENSRNOG00000018044	1 retrocopy	retro_rnor_542,
Tursiops truncatus	ENSTTRG00000011113	1 retrocopy	retro_ttru_1844,