RetrogeneDB - Retrocopy retro_btau

						
>retro_btau_103
ATGGCCCAGGAGAAGATGGAGCTAGACCTGGAGCTCCCTCCGGGCTCAGGTGGGAGCCCGGCGGAGGGCAGCAGCAGTGG

CGGCGGCGGGGGCCTCAGGAGATCTAACAGCGCCCCCCTGATCCACGGCCTCAGTGACACTTCTCCGGTGTTCCAGGCCG

AGGCGCCGAGCGCCAGGCGAAACAGCACAACGTTCCCGAACCGCCACGGCCTGCTTCTGCCGGCCTCCCCAGTCCGCATG

CACAGCAGCCGCTTGCACCAGATCAAACAGGAGGAGGGCATGGACTTGATCAATCGAGAGACTGTCCACGAGCGCGAGGT

GCAGAACGCAATGCAGATAAGCCACTCCTGGGAGGAAAGTTTCAGCCTGAGCGACAACGACGTGGAGAAATCTGCCTCCC

CGAAACGCATCGATTTCATTCCGGTGTCGCCAGCACCGTCGCCTACCCGGGGAATTGGAAAGCAGTGTTTTTCACCATCC

TTGCAAAGTTTTGTGAGTAGCAATGGATTGCCTCCAAGTCCTGTTCCCAGCCCAACGACCCGATTTACTACCCGGAGAAG

CCAGAGTCCCATTAATTGCATTAGACCAAGTGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGAGTATCAGC

CAAAGAGATTTTTCCAAGGCATCACCAACATGCTTTCTTCTGACGTTGCGCAGCTGTCAGATCCGGGTGTGTGTGTATCT

TCCGATACCCTTGATGGAAACAGCAGCAGCGCCGGATCTTCTTGTAACTCACCAGCGAAAGTCAGCACTACCACCGACTC

TCCTGTGTCGCCTGCCCAAGCGGCCTCTCCATTTATTCCAGTAGATGAACTTTCATCTAAGTGA

ORF - retro_btau_103 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	72.25 %
Parental protein coverage:	83.13 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalGGTLRRSNSAPLIHGLSNWVGAFNPFTFKCVRNSKSEETRHLPLLSTSPNRIPSSRLHQIKREEGMDIMN
		GG.LRRSNSAPLIHGLS.....F........RNS.....RH..LL..SP.R..SSRLHQIK.EEGMD..N
RetrocopyGGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPNRHGLLLPASPVRMHSSRLHQIKQEEGMDLIN
ParentalRETAHEREVQTAMQISQSWDESLSLSDSDFDKQEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQMFV
		RET.HEREVQ.AMQIS.SW.ES.SLSD.D....EK..SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.FV
RetrocopyRETVHEREVQNAMQISHSWEESFSLSDNDV---EKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFV
ParentalSSSGLPPSPVPSP-RRFST-RSQSPIKCIRPSVLAPLKRKGEMETESQPKRLFQGTTNMLSPEAAQLSD
		SS.GLPPSPVPSP..RF.T.RSQSPI.CIRPSVL.PLKRK.EMETE.QPKR.FQG.TNMLS...AQLSD
RetrocopySSNGLPPSPVPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSD

							

							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
ERP005899_liver	5 .70 RPM	1 .30 RPM
ERP005899_muscle	5 .75 RPM	4 .17 RPM
SRP017611_brain	8 .63 RPM	8 .22 RPM
SRP017611_kidney	8 .42 RPM	6 .34 RPM
SRP017611_liver	5 .51 RPM	2 .04 RPM
SRP030211_testis	2 .63 RPM	2 .84 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_btau_103 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CO261343	45177271	45177498	100	227	0	227

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_103 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_btau_103 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_35
Mus musculus	retro_mmus_22
Rattus norvegicus	retro_rnor_651
Oryctolagus cuniculus	retro_ocun_205
Canis familiaris	retro_cfam_181
Equus caballus	retro_ecab_91

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_btau_103
Retrocopy location	Organism:	*Cow (Bos taurus)*
	Coordinates:	8:45177297..45178161(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSBTAG00000021586
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	FAM122B
	Ensembl ID:	ENSBTAG00000001886
	Aliases:	None
	Description:	protein FAM122B [Source:RefSeq peptide;Acc:NP_001077263]

Parental	GGTLRRSNSAPLIHGLSNWVGAFNPFTFKCVRNSKSEETRHLPLLSTSPNRIPSSRLHQIKREEGMDIMN
	GG.LRRSNSAPLIHGLS.....F........RNS.....RH..LL..SP.R..SSRLHQIK.EEGMD..N
Retrocopy	GGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPNRHGLLLPASPVRMHSSRLHQIKQEEGMDLIN

Parental	RETAHEREVQTAMQISQSWDESLSLSDSDFDKQEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQMFV
	RET.HEREVQ.AMQIS.SW.ES.SLSD.D....EK..SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.FV
Retrocopy	RETVHEREVQNAMQISHSWEESFSLSDNDV---EKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFV

Parental	SSSGLPPSPVPSP-RRFST-RSQSPIKCIRPSVLAPLKRKGEMETESQPKRLFQGTTNMLSPEAAQLSD
	SS.GLPPSPVPSP..RF.T.RSQSPI.CIRPSVL.PLKRK.EMETE.QPKR.FQG.TNMLS...AQLSD
Retrocopy	SSNGLPPSPVPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSD

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

RetrogeneDB ID:

retro_btau_103