RetrogeneDB - Retrocopy retro_cjac

						
>retro_cjac_594
CTCAGGAGGTCTAACAGCGCCCCCCTCATCCACGGCCTCAGTGACACTTCGCCGGTGTTCCAGGCCGAGGCGCCGAGCGC

CAGGCGGAACAGCACAACGTTCTCGAGCCGCCACGGCCTGCTGCTACCGGCCTCCCCTGTCCGCATGCACAGCAGCCGCT

TGCACCAGATCAAACAAGAAGAGGGCATGGACTTAATCAACCGAGAGACGGTCCACGAGCGGGAGGTGCAGACCGCAATG

CAGATAAGCCACTCCTGGGAGGAAAGTTTCAGCCTGAGTGACAACGACGTGGAGAAATCCGCCTCCCCCAAGCGCATCGA

TTTCATTCCTGTGTCACCAGCACCGTCACCCACTCGGGGAATTGGGAAGCAGTGTTTTTCGCCATCCTTGCAAAGTTTTG

TAAGTAGCAACGGATTGCCTCCAAGCCCTATTCCCAGCCCAACGACCCGATTTACCACCCGGAGAAGCCAGAGCCCTATC

AATTGCATTAGACCAAGTGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGAATATCAGCCAAAGAGATTTTT

CCAGGGCATCACCAACATGCTTTCTTCTGACGTTGCACAGCTGTCAGATCCTGGTGTGTGTGTATCTTCGGATACCCTTG

ATGGAAACAGCAGCAGTGCCGGATCTTCTTGTAACTCACCAGCGAAAGTCAGCACTACCACCGACTCTCCTGTGTCACCT

GCCCAAGTGGCTTCTCCATTTATTCCACTAGATGAACTTTCGTCTAAG

ORF - retro_cjac_594 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	68.2 %
Parental protein coverage:	89.93 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalLRRSSSAPLIHGLSDLSEVFQPYTRT-RRNSTTIMSSHSLLLSSSPNRIPSSRLHQIKREEGLDMMNRET
		LRRS.SAPLIHGLSD.S.VFQ......RRNSTT..S.H.LLL..SP.R..SSRLHQIK.EEG.D..NRET
RetrocopyLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFSSRHGLLLPASPVRMHSSRLHQIKQEEGMDLINRET
ParentalAHEREIQSAMQISQSWDESLSLSDSDFDKQEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQMFVSSS
		.HERE.Q.AMQIS.SW.ES.SLSD.D....EK..SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.FVSS.
RetrocopyVHEREVQTAMQISHSWEESFSLSDNDV---EKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFVSSN
ParentalGLPPSPVPS-TRRFSSRRSQSPVKCIRPSALGPLKRKGEMETESQPKRLFQGTTNMLSPEAAQLSDDSPN
		GLPPSP.PS.T.RF..RRSQSP..CIRPS.LGPLKRK.EMETE.QPKR.FQG.TNMLS...AQLSD..P.
RetrocopyGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSD--PG
ParentalFVFSSDILDGSSSSSGLSSDPLAKGSATAESPVACSNSCSSFILMDDLSPK
		...SSD.LDG.SSS.G.S....AK.S.T..SPV......S.FI..D.LS.K
RetrocopyVCVSSDTLDGNSSSAGSSCNSPAKVSTTTDSPVSPAQVASPFIPLDELSSK

							

							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
SRP051959_colon	3 .19 RPM	2 .86 RPM
SRP051959_heart	3 .32 RPM	4 .37 RPM
SRP051959_kidney	3 .71 RPM	6 .01 RPM
SRP051959_liver	2 .86 RPM	3 .10 RPM
SRP051959_lung	5 .30 RPM	6 .49 RPM
SRP051959_lymph_node	2 .17 RPM	7 .85 RPM
SRP051959_skeletal_muscle	4 .04 RPM	2 .84 RPM
SRP051959_spleen	3 .74 RPM	6 .49 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_594 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_594 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cjac_594 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_185

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_cjac_594
Retrocopy location	Organism:	*Marmoset (Callithrix jacchus)*
	Coordinates:	1:100397179..100397947(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSCJAG00000001765
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	FAM122B
	Ensembl ID:	ENSCJAG00000004313
	Aliases:	None
	Description:	family with sequence similarity 122B [Source:HGNC Symbol;Acc:30490]

Parental	LRRSSSAPLIHGLSDLSEVFQPYTRT-RRNSTTIMSSHSLLLSSSPNRIPSSRLHQIKREEGLDMMNRET
	LRRS.SAPLIHGLSD.S.VFQ......RRNSTT..S.H.LLL..SP.R..SSRLHQIK.EEG.D..NRET
Retrocopy	LRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFSSRHGLLLPASPVRMHSSRLHQIKQEEGMDLINRET

Parental	AHEREIQSAMQISQSWDESLSLSDSDFDKQEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQMFVSSS
	.HERE.Q.AMQIS.SW.ES.SLSD.D....EK..SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.FVSS.
Retrocopy	VHEREVQTAMQISHSWEESFSLSDNDV---EKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFVSSN

Parental	GLPPSPVPS-TRRFSSRRSQSPVKCIRPSALGPLKRKGEMETESQPKRLFQGTTNMLSPEAAQLSDDSPN
	GLPPSP.PS.T.RF..RRSQSP..CIRPS.LGPLKRK.EMETE.QPKR.FQG.TNMLS...AQLSD..P.
Retrocopy	GLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSD--PG

Parental	FVFSSDILDGSSSSSGLSSDPLAKGSATAESPVACSNSCSSFILMDDLSPK
	...SSD.LDG.SSS.G.S....AK.S.T..SPV......S.FI..D.LS.K
Retrocopy	VCVSSDTLDGNSSSAGSSCNSPAKVSTTTDSPVSPAQVASPFIPLDELSSK

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

RetrogeneDB ID:

retro_cjac_594