RetrogeneDB ID: retro_cpor_661

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_212:496051..497047(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000011784
• Aliases: None
• Description: None

Sequence

>retro_cpor_661
AGCTTTGCTTCTGATAATTTTTGCAAACACGAGACCACAGGCAGCCCAAGGGCTGCAGGACCCGCAGCCAGGGCAGGTCC
TCTAGCCCTCTTAGGGTGGCATGAATTTCCCAGTGCCAGTGCGTAGCATCAGGGCGACACCCGAAAAAAAGCCAGGGCAC
TCCCCAACCCCCAGAGAATTCTGCCACCATTTCCAACTCCGATTCAGAAGATGAAAGTGGCATGAACTTTCTGAAAAAAT
GGGCCTTAAATATAAAATAAAGCAAAGCCATGCTTGCAAAACTCATGTCAGAATTAGGAAGTTTTCTTGGCTCATTTTCT
GGAAGACCTTCTGTCCTGGGCCCCAGATCAGTGCGTTCCCAGGCGCCCCTGAGGCGCACATTCCCAGGTGCGGCTTCCAG
GAGGAACCCGGAGCGCAGAACCGGCTGCTTACCAGGTCCAGGTCTCGGATTCTGGGGTCCCCGAGCGCTCTCCCCGCTGA
GGAGGAGGAAGAAGAGGAAGACGGAAGACCACAAGTACATGCTCGTGAGGAAAAGGAAGGCCTTGGATGCACTGGACGAT
GACATGCCGGGTCGTCGCCTGGGATCCACGACCCTTCCACATGTAATTCGTCCGGTAGAAGAGATCACAGCAATGAGTTG
GAGAACATCTGTAGCAACTCCCGAGAGAAGATCTAAGATCGCTCACCAGGCTCTACCTGCCGTCAGTGCGGTCAGAAAAC
TATTAACACCAAAACAAACTGCAGGCACCCCGACAGCTGGGGCATTCCAGGCCAGTTCTATTGCCCTGCCTTCAGAATCG
CTATGGGGAAGAGATCAGGGATGCACTGCTGGACCGGGACTGCCCACCTTGTCGAGGGATCTGTAACTGCAGTTTCTGTT
GCCAGTGAGATGGATAGTGTGCAGTTGGGGTCCTTGAGTATTTAGCTGAATTCCATGGCTTTGGGGATGTGCATGCTTAT
TTGAAGAGTCTGAAACAGGAGTTTGAAATGCAAGTA

Alignment

ORF - retro_cpor_661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.21 %
• Parental protein coverage: 90.88 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  SFASDNFAN-TRLQAAREGCRTRSQGRLSGPLRVA-MKFPVRVHSTRATTNKKPA-PPKPPENSDIISIS
          SFASDNF...TR......GCRTRSQGR.S.PLRVA.M.FPV.V.S.RAT..KKP...P.PPENS..IS.S
Retrocopy SFASDNFCK<TRDHRQPKGCRTRSQGRSSSPLRVA<MNFPVPVRSIRATPEKKPG>TPQPPENSATISNS

Parental  DSEDESGVNFLEKRALNIKQNKAMLAKLMSELESFPGSFSGRPSVPGPRSL-SKTPRRRTFPRMAARRNP
          DSEDESG.NFL.K.ALNIK..KAMLAKLMSEL.SF.GSFSGRPSV.GPRS..S..P.RRTFP..A.RRNP
Retrocopy DSEDESGMNFLKKWALNIK*SKAMLAKLMSELGSFLGSFSGRPSVLGPRSVRSQAPLRRTFPGAASRRNP

Parental  ERRA-RPLTRSRSRILGSLSALPTEEE--EEE-EDDKYMLVRKRKALDALYSQDDDMPRSRRPGSMTLPH
          ERR..R.LTRSRSRILGS.SALP.EEE..EE..ED.KYMLVRKRKALDAL...DDDMP..RR.GS.TLPH
Retrocopy ERRT<RLLTRSRSRILGSPSALPAEEEEEEED>EDHKYMLVRKRKALDAL---DDDMP-GRRLGSTTLPH

Parental  IIRPVEEIT-EDELENICSNSREKIYNRSLGSTCHQCRQKTIDTKTNCRNPDCWGIRGQF-CGPCLRNRY
          .IRPVEEIT...ELENICSNSREKI..RS.GSTC.QC.QKTI.TKTNCR.PD.WGI.GQF...PCL.NRY
Retrocopy VIRPVEEIT<SNELENICSNSREKI*DRSPGSTCRQCGQKTINTKTNCRHPDSWGIPGQF<LLPCLQNRY

Parental  GEEVRDALLDPDWHCPPCRGICNCSFCRQRDGRCATGVLVYLAKYHGFGNVHAYLKSPHSLKQEFEMQV
          GEE.RDALLD.D..CPPCRGICNCSFC.Q.DG.CA.GVL.YLA..HGFG.VHAYLKS...LKQEFEMQV
Retrocopy GEEIRDALLDRD--CPPCRGICNCSFCCQ*DG*CAVGVLEYLAEFHGFGDVHAYLKS---LKQEFEMQV

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	0.92 RPM
SRP017611_kidney	0.00 RPM	4.92 RPM
SRP017611_liver	0.00 RPM	12.14 RPM
SRP040447_lung	0.00 RPM	2.14 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.64 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_661 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_661 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
Callithrix jacchus	ENSCJAG00000007809	1 retrocopy	retro_cjac_4087,
Cavia porcellus	ENSCPOG00000011784	2 retrocopies	retro_cpor_661 , retro_cpor_691,
Homo sapiens	ENSG00000144354	1 retrocopy	retro_hsap_3438,
Mus musculus	ENSMUSG00000055612	2 retrocopies	retro_mmus_1493, retro_mmus_1494,
Nomascus leucogenys	ENSNLEG00000005787	1 retrocopy	retro_nleu_2295,
Pan troglodytes	ENSPTRG00000012645	1 retrocopy	retro_ptro_2331,
Ictidomys tridecemlineatus	ENSSTOG00000009026	1 retrocopy	retro_itri_369,