RetrogeneDB ID: retro_cpor_151

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:31888981..31889610(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000025760
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAA60
• Ensembl ID: ENSCPOG00000005731
• Aliases: None
• Description: None

Sequence

>retro_cpor_151
ATGAAGGACGTGGTGCCTTCTCGTGCCCTCAGCGAGGTCTGCCTGTGCCTTCTCTGCCGTGATGACACAGACACCGTAAA
GCACCTGTGCAGGGACTGGCTCCCCACCGAGTACCCAGACTCATGGTACCGTGATATCACATCCAACAAGAAGTTCGTCT
CTCTGGCTGCCACTGTGTGGTACCAGGGGTACCATTATGGGGATGATGGCAGCTGAAATTAAGAGCAGGACTAAAACACA
TGAAGAGGATGGAGATATCCTAGCCTCCAACTTCTCTGTGGACACACAGAATGTGTACATTCTAAGTCTGGGAGTAGTGA
AGGGATTCAGAAAGTATGGTTCCCTTTCACTTGGAAGTTTAAAGAATCACATATCAACCACTGTCCATGATCACAGCAAA
GCCATCTACCTACACATCCTCACCACCAACAACGTGGCAATAAACTACAAAAACAGAGGCTTTAGGCAGCATCACTCTGC
CTGATTACTACTCCATCCAAGGGGTTCTCAAAGATGGCTTCACTTATGTCCTTTATATCAATACTGGCCACCCTCTCTGG
ACTATCTTAGAATACGTCCAGCATCTGGACTCAGCAGTCACCAACCTGAGCCCCTGCTCCATCTCACAC

Alignment

ORF - retro_cpor_151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.81 %
• Parental protein coverage: 87.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTEVVPSSALSEVSLRLLCHDDIDTVKHLCSDWFPIEYPDSWYRDITSNKKFFSLAAT--YRG-AIVGMI
          M..VVPS.ALSEV.L.LLC.DD.DTVKHLC.DW.P.EYPDSWYRDITSNKKF.SLAAT..Y.G..I.GM.
Retrocopy MKDVVPSRALSEVCLCLLCRDDTDTVKHLCRDWLPTEYPDSWYRDITSNKKFVSLAATVWYQG>TIMGMM

Parental  VAEIKSRTKIHKEDGDILASNFSVDTQVAYILSLGVVKEFRKHGIGSLLLESLKDHISTTAQDHCKAIYL
          .AEIKSRTK.H.EDGDILASNFSVDTQ..YILSLGVVK.FRK...GSL.L.SLK.HISTT..DH.KAIYL
Retrocopy AAEIKSRTKTHEEDGDILASNFSVDTQNVYILSLGVVKGFRKY--GSLSLGSLKNHISTTVHDHSKAIYL

Parental  HVLTTNNTAINFYENRDFRQHHYL-PYYYSIRGVLKDGFTYVLYINGGHPPWTILDYIQHLGSALANLSP
          H.LTTNN.AIN.Y.NR.FRQHH....YY.SI.GVLKDGFTYVLYIN.GHP.WTIL.Y.QHL.SA..NLSP
Retrocopy HILTTNNVAIN-YKNRGFRQHHSA>DYY-SIQGVLKDGFTYVLYINTGHPLWTILEYVQHLDSAVTNLSP

Parental  CSIPH
          CSI.H
Retrocopy CSISH

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	37.27 RPM
SRP017611_kidney	0.00 RPM	50.25 RPM
SRP017611_liver	0.00 RPM	23.29 RPM
SRP040447_lung	0.00 RPM	33.59 RPM
SRP040447_skeletal_muscle	0.00 RPM	23.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_151 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_151 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005731	1 retrocopy	retro_cpor_151 ,
Echinops telfairi	ENSETEG00000014209	1 retrocopy	retro_etel_1344,
Myotis lucifugus	ENSMLUG00000017721	1 retrocopy	retro_mluc_1295,