RetrogeneDB ID: retro_cpor_1157

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_50:7450199..7451022(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP46
• Ensembl ID: ENSCPOG00000007660
• Aliases: None
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:H0VAL5]

Sequence

>retro_cpor_1157
CTGTGCTTCTGCCTGCCACTTTGTGAGAAAGTGCTGGCATCCAAGGCCCAGCAGAATAAACAAGGAAAGCTTGCTGACAT
GCCTGGCAAACCTTTTCCACAGCACTGCCACGCAGAAGAAGGTGGGCATAATCCCACCCAAGAAGTTCATTTCAAGACTG
AGAAAGGAGAATGATCTCTTTGATAACTACATGAGGCAGGATGCTTGTGAATTTTTAAATTATTTCCTGAACACTATTGC
ACACATTATAGGAAGAGAAGAAACAAGAAAAGCAAAGTGGAAAGTTTAAAAATGGCAACATGAATGAACTTTCAGAGAAT
AATAAACCAGAACTCACCTGGGCCCATGAGAGTTTTCAGGGCATTCTCGCCAATGAAACCAGATGTTCGAACTGTGAATT
CTTTACTAGCAAAGATGAAGATTCCTTGACCTTTCTGTTGATGTGGAGCAGGACCTTCTATTACCTACTGTCTGAGGGAC
TTCAGCAGCACAGAAACACTGTGTAGTGAACAAAAATGTTATTATGAGACATGCTTCAGCAAACAGGAGGCCAGGAAAGG
ATGGGGGGAAAAAGCTGCCCATGATTTTGGCCCTGCACCGTAAGTGGTTCAAATACATAGAGCAGCTCCATAGGCACACC
AAGCCGTCTTACTGGGCGATCTTCCCTCTGGATTTCCAGCTCGTGACACCTCCAGTGATACCATGAGCCTGGACTGATGT
GTGACCTGATCCCTGTGTTCTTTCATTGTGCCATGGCCATAATTGTGGGCATTATATTACTGTAGTGAGAAGTCATGCTT
TCTGGCTTTTATTTGATGATGAT

Alignment

ORF - retro_cpor_1157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.78 %
• Parental protein coverage: 75.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  LYFCRPFRENVLAYKAQQKK-KENLLTCLADLFHSIATQKKKVGVIPPKKFISRLRKENDLFDNYMQQDA
          L.FC.P..E.VLA.KAQQ.K.KE.LLTCLA.LFHS.ATQKK.VG.IPPKKFISRLRKENDLFDNYM.QDA
Retrocopy LCFCLPLCEKVLASKAQQNK>KESLLTCLANLFHSTATQKK-VGIIPPKKFISRLRKENDLFDNYMRQDA

Parental  HEFLNYLLNTIADIL-QEEKKQEKQNGKLKNGNMNEPAENNKPELTWVHEIFQGTLTNETRCLNCETVSS
          .EFLNY.LNTIA.I...E.K.QEKQ.GK.KNGNMNE..ENNKPELTW.HE.FQG.L.NETRC.NCE...S
Retrocopy CEFLNYFLNTIAHII>EEKK-QEKQSGKFKNGNMNELSENNKPELTWAHESFQGILANETRCSNCEFFTS

Parental  KDED-FLDLSVDVEQN-TSITHCLRDFSNTETLCSEQKYYCEMCCSKQEA-QKRMRVK-KLPMILALHLK
          KDED.FLDLSVDVEQ...SIT.CLRDFS.TETLCSEQK.Y.E.C.SKQEA.Q.RM..K.KLPMILALH.K
Retrocopy KDED<FLDLSVDVEQD<PSITYCLRDFSSTETLCSEQKCYYETCFSKQEA<QERMGGK<KLPMILALHRK

Parental  RFKYMEQLHRYTKLSYRVVFPLELRLF-NTSSDAVNLD-RMYDLVAVVVHCG-SGPNRGHYITIVKSHGF
          .FKY.EQLHR.TK.SY...FPL...L...TSSD...LD..M.DL..V..HC...G.N.GHYIT.V.SH.F
Retrocopy WFKYIEQLHRHTKPSYWAIFPLDFQLV<DTSSDTMSLD<LMCDLIPVFFHCA<HGHNCGHYITVVRSHAF

Parental  WLLFDDD
          WLLFDDD
Retrocopy WLLFDDD

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	21.05 RPM
SRP017611_kidney	0.00 RPM	4.82 RPM
SRP017611_liver	0.00 RPM	1.48 RPM
SRP040447_lung	0.00 RPM	18.66 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.81 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1157 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1157 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007660	1 retrocopy	retro_cpor_1157 ,
Gorilla gorilla	ENSGGOG00000017197	3 retrocopies	retro_ggor_1767, retro_ggor_2223, retro_ggor_2937,