RetrogeneDB - Retrocopy retro_cpor

						
>retro_cpor_80
ATGGCTCAGGAGAAGATGGAGCTGGATTTGGAGCTGCCTCCGGGTACGGGCGGGAGCCCGGCGGAGAGCGGCAGCAGTGG

TGGTGGCGGGGGCCTCAGGAGGTCTAACAGCGCCCCCCTGATCCACGGCCTCAGTGACACTTCGCCGGTGTTCCAGGCCG

AGGCGCCGAGCGCTAGGAGGAACAGCACAACGTTCCCAAGCCGCCACGGCCTGCTGCTACCTGCCTCCCCCGTCCGCATG

CACAGCAGCCGCTTGCACCAGATCAAACAGGAGGAGGGCATGGACTTGATCAACCGAGAGACGGTCCACGAGCGCGAGGT

GCAGACCGCAATGCAGATAAGCCACTCCTGGGAGGAAAGTTTCAGTCTAAGTGACAACGATGTGGAGAAATCCGCCTCCC

CAAAGCGCATCGATTTCATTCCAGTATCACCAGCACCGTCTCCCACCCGGGGAATTGGAAAGCAGTGTTTTTCACCATCC

TTGCAAAGTTTTGTGAGTAGCAATGGATTACCTCCAAGCCCTATTCCCAGCCCAACTACCCGATTTACCACCCGGCGAAG

CCAGAGCCCCATCAACTGCATTAGACCAAGTGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGAGTATCAGC

CAAAGAGATTTTTCCAGGGCATCACCAACATGCTTTCTTCTGACGTTGCACAGCTGTCAGACCCCGGCGTGTGTGTGTCT

TCGGATACCCTTGATGGAAACAGCAGCAGGGCAGGATCTTCTTGTAACTCACCAGCGAAAGTCAGCACCACCACCGACTC

TCCTGTGTCACCTACCCAAGCAGCCTCTCCCTTTATTCCAGTAGATGAACTTTCATCTAAGTGA

ORF - retro_cpor_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	66.02 %
Parental protein coverage:	91.07 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalGSTLRRSNSAPLIHGLSDFSQVFQPYSFKTRRNSTTIMNSRTFLLPSSTNRIPSSRLHQIKREEGLDIMN
		G..LRRSNSAPLIHGLSD.S.VFQ......RRNSTT.......LLP.S..R..SSRLHQIK.EEG.D..N
RetrocopyGGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPSRHGLLLPASPVRMHSSRLHQIKQEEGMDLIN
ParentalRETAHEREVQTAMQISQSWDESLNLSDNDFDKPEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQMFV
		RET.HEREVQTAMQIS.SW.ES..LSDND....EK..SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.FV
RetrocopyRETVHEREVQTAMQISHSWEESFSLSDNDV---EKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFV
ParentalSSSGLPSSTFGTP-RRFSTRRSQSPVKCIRPSVLGPIKRKGEMETESQPKRLFQGTTNMLSPDAAQLSDL
		SS.GLP.S....P..RF.TRRSQSP..CIRPSVLGP.KRK.EMETE.QPKR.FQG.TNMLS.D.AQLSD.
RetrocopySSNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSDP
ParentalNSCFVLSPDVMDGSSSSSGLSSDSLATGSAPAESPVACSNSCSPFM
		..C...S.D..DG.SS..G.S..S.A..S....SPV......SPF.
RetrocopyGVC--VSSDTLDGNSSRAGSSCNSPAKVSTTTDSPVSPTQAASPFI

							

							Legend:
							
								*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

						

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	6 .27 RPM	22 .89 RPM
SRP017611_kidney	6 .28 RPM	13 .92 RPM
SRP017611_liver	4 .40 RPM	4 .88 RPM
SRP040447_lung	6 .99 RPM	15 .18 RPM
SRP040447_skeletal_muscle	5 .09 RPM	3 .15 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_80 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_80 was not experimentally validated.

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.

Parental genes homology:

Parental genes homology involve 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001311	1 retrocopy	retro_amel_105,
Bos taurus	ENSBTAG00000001886	1 retrocopy	retro_btau_103,
Canis familiaris	ENSCAFG00000018882	1 retrocopy	retro_cfam_181,
Callithrix jacchus	ENSCJAG00000004313	1 retrocopy	retro_cjac_594,
Cavia porcellus	ENSCPOG00000011218	1 retrocopy	retro_cpor_80 ,
Equus caballus	ENSECAG00000018643	1 retrocopy	retro_ecab_91,
Felis catus	ENSFCAG00000024842	1 retrocopy	retro_fcat_1575,
Myotis lucifugus	ENSMLUG00000007988	1 retrocopy	retro_mluc_382,
Macaca mulatta	ENSMMUG00000016948	1 retrocopy	retro_mmul_185,
Mustela putorius furo	ENSMPUG00000012690	1 retrocopy	retro_mputfur_64,
Mus musculus	ENSMUSG00000036022	1 retrocopy	retro_mmus_22,
Rattus norvegicus	ENSRNOG00000050146	1 retrocopy	retro_rnor_651,
Sus scrofa	ENSSSCG00000012685	1 retrocopy	retro_sscr_60,
Ictidomys tridecemlineatus	ENSSTOG00000006261	1 retrocopy	retro_itri_61,

	RetrogeneDB ID:	retro_cpor_80
Retrocopy location	Organism:	*Guinea Pig (Cavia porcellus)*
	Coordinates:	scaffold_21:20060398..20061262(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSCPOG00000003280
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	FAM122B
	Ensembl ID:	ENSCPOG00000011218
	Aliases:	None
	Description:	None

Parental	GSTLRRSNSAPLIHGLSDFSQVFQPYSFKTRRNSTTIMNSRTFLLPSSTNRIPSSRLHQIKREEGLDIMN
	G..LRRSNSAPLIHGLSD.S.VFQ......RRNSTT.......LLP.S..R..SSRLHQIK.EEG.D..N
Retrocopy	GGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPSRHGLLLPASPVRMHSSRLHQIKQEEGMDLIN

Parental	RETAHEREVQTAMQISQSWDESLNLSDNDFDKPEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQMFV
	RET.HEREVQTAMQIS.SW.ES..LSDND....EK..SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.FV
Retrocopy	RETVHEREVQTAMQISHSWEESFSLSDNDV---EKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFV

Parental	SSSGLPSSTFGTP-RRFSTRRSQSPVKCIRPSVLGPIKRKGEMETESQPKRLFQGTTNMLSPDAAQLSDL
	SS.GLP.S....P..RF.TRRSQSP..CIRPSVLGP.KRK.EMETE.QPKR.FQG.TNMLS.D.AQLSD.
Retrocopy	SSNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSDP

Parental	NSCFVLSPDVMDGSSSSSGLSSDSLATGSAPAESPVACSNSCSPFM
	..C...S.D..DG.SS..G.S..S.A..S....SPV......SPF.
Retrocopy	GVC--VSSDTLDGNSSRAGSSCNSPAKVSTTTDSPVSPTQAASPFI

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_cpor_80