RetrogeneDB - Retrocopy retro_sscr

						
>retro_sscr_60
CATGCGCAAGGCACGAGCCCGCTGACAGATTCGCGGTGGCGGTGGTGGCGGCGGCGGCCCTGTATTGCGGGGAATGGGAA

TCCTAGGTCTCTGACTGAGCACCGCCCCCGCCTCCCTGCCCCCGACATGGCTCAGGAGAAGATGGAGCTAGACCTGGAGC

TGCCTCCGGGCACGGGTGGGAGCCCGGCGGAGGGCGGCGGCAGTGGTGGCGGCGGGGGCCTCAGGAGGTCTAACAGCGCC

CCCCTCATCCACGGCCTCAGTGACACTTCGCCGGTGTTCCAGGCCGAGGCGCCGAGCGCCAGGCGGAACAGCACAACGTT

CCCGAACCGCCACGGCCTGCTGCTACCAGCCTCCCCCGTCCGCATGCACAGCAGCCGCTTGCACCAGATCAAACAAGAGG

AGGGCATGGACTTGATCAACCGAGAGACGGTCCACGAGCGCGAGGTGCAGAACGCAATGCAGATAAGCCACTCCTGGGAG

GAAAGTTTCAGCCTGAGTGACAACGACGTGGAGAAATCCGCCTCCCCGAAACGCATTGATTTCATTCCAGTGTCACCAGC

ACCGTCACCCACCCGGGGAATTGGAAAGCAGTGTTTTTCACCGTCTTTGCAAAGTTTTGTGAGTAGCAATGGATTGCCTC

CAAGTCCTATTCCCAGCCCAACGACCCGATTTACTACCCGCAGAAGCCAGAGTCCCATTAATTGCATTAGACCAAGTGTT

CTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGAATATCAGCCAAAGAGATTTTTCCAGGGCATCACCAACATGCT

TTCTTCTGACGTTGCACAACTGTCAGATCCTGGTGTGTGTGTATCTTCCGATACCCTTGATGGAAACAGCAGCAGTGCCG

GATCTTCTTGTAACTCACCAGCGAAAGTCAGCACTACCACCGACTCTCCTGTATCGCCTGCCCAAGCGGCGTCTCCATTT

ATTCCAGTAGATGAACTTTCATCTAAGTGA

ORF - retro_sscr_60 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	73.08 %
Parental protein coverage:	83.06 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalGGTLRRSNSAPLIHGLSDLSQVFQPYTFRTRRNSTIIMSRPGLLLSSSPNRIPSSRLHQIKREEGMDMMN
		GG.LRRSNSAPLIHGLSD.S.VFQ......RRNST....R.GLLL..SP.R..SSRLHQIK.EEGMD..N
RetrocopyGGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPNRHGLLLPASPVRMHSSRLHQIKQEEGMDLIN
ParentalRETAHEREMQSAMQISQSWDESLSLSDSDFDKEKLYSPKRIDFTPVSPAPSPTRGLGKQCFSPSLQMFVS
		RET.HERE.Q.AMQIS.SW.ES.SLSD.D...EK..SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.FVS
RetrocopyRETVHEREVQNAMQISHSWEESFSLSDNDV--EKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFVS
ParentalSSGLPPSPVSSP--RRFSRRSQSPVKCIRPSVLGPLKRKGEMETESQPKRLFQGTTSMLSPEATQLSD
		S.GLPPSP..SP..R...RRSQSP..CIRPSVLGPLKRK.EMETE.QPKR.FQG.T.MLS....QLSD
RetrocopySNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSD

							

							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
SRP014902_placenta	9 .69 RPM	117 .07 RPM
SRP014902_testis	15 .28 RPM	29 .99 RPM
SRP018288_heart	6 .71 RPM	7 .26 RPM
SRP018288_kidney	9 .26 RPM	13 .99 RPM
SRP018288_liver	7 .52 RPM	7 .52 RPM
SRP018288_lung	29 .12 RPM	26 .37 RPM
SRP018856_adipose	9 .67 RPM	23 .07 RPM
SRP035408_brain	6 .00 RPM	4 .61 RPM
SRP035408_liver	4 .73 RPM	6 .58 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_60 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_60 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_sscr_60 has 0 orthologous retrocopies within eutheria group .

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_sscr_60
Retrocopy location	Organism:	*Pig (Sus scrofa)*
	Coordinates:	1:248523792..248524782(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSSSCG00000005245
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	FAM122B
	Ensembl ID:	ENSSSCG00000012685
	Aliases:	None
	Description:	family with sequence similarity 122B [Source:HGNC Symbol;Acc:30490]

Parental	GGTLRRSNSAPLIHGLSDLSQVFQPYTFRTRRNSTIIMSRPGLLLSSSPNRIPSSRLHQIKREEGMDMMN
	GG.LRRSNSAPLIHGLSD.S.VFQ......RRNST....R.GLLL..SP.R..SSRLHQIK.EEGMD..N
Retrocopy	GGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPNRHGLLLPASPVRMHSSRLHQIKQEEGMDLIN

Parental	RETAHEREMQSAMQISQSWDESLSLSDSDFDKEKLYSPKRIDFTPVSPAPSPTRGLGKQCFSPSLQMFVS
	RET.HERE.Q.AMQIS.SW.ES.SLSD.D...EK..SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.FVS
Retrocopy	RETVHEREVQNAMQISHSWEESFSLSDNDV--EKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFVS

Parental	SSGLPPSPVSSP--RRFSRRSQSPVKCIRPSVLGPLKRKGEMETESQPKRLFQGTTSMLSPEATQLSD
	S.GLPPSP..SP..R...RRSQSP..CIRPSVLGPLKRK.EMETE.QPKR.FQG.T.MLS....QLSD
Retrocopy	SNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSD

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

RetrogeneDB ID:

retro_sscr_60