RetrogeneDB - Retrocopy retro_cjac

                        
>retro_cjac_2678
ATGGAGAACACTGAAAACTCGGTGGATTCAAAATCCATTAAAAATTTGGAACCAAAGATCAGACAAGGAAGCAAATCAAT

GGACTCTGGAATATCCTTGGACAATAGTTGTAAAATGGATTATCCTCAAATGGGTTTATGTATAATAATAATGAGAACTT

TCATAAAAGCACTGGAATGGCATCTCAGTCTGGTACAGATGTTGATGTAGCAAACCTCAGGGAAACATTCATGAAGTTGA

AAGATGAAGTCAGGAATAAAAATGATCTTACACATGAAGAAATTGTGGAATTGATGTGTAATGTTTCTGAAGAAGGTGAC

AGCAAAAGGAGCAGTTTTGCTTGTGTGCTTCCGAGCCATGGTGAAGAAGAAATAATTTTTGGAACAAATGGACCTATTGA

CCTGAAAAAAATAGCAAGCTTTTTCAGAGGGGATTGTTGTAGGAGTCTAACTGGAAAACCCAAATTTTTCCTTATTCAGG

CCTGCCATGGTATAGAACTGGACTGTGGCATTGAGATAGACAGCGGTGTTGATGATGGCATGGTGCGTCATAAAACACCA

GTGGAGGCCGACCTCTTGCACGCACACTCCACAGCACCTGGGTATCATTCTTGGTGAAATTCAAAGGATGGCTCCTGGTT

TATCCAGTCACTTTGTGCCATGCTGGAACAGTGCGCCCACAAGCTTGCGTTTATGCACAAGGTTAACCAAAGGTGGCAAC

AGAATTTGAGTCCTTTTCCCTTGACGCTACTTTTAATGCAAAGAAACAGATTCCATGTATTGTTTCCATGCTTACAAAAG

AACTGTATTTTTAT

ORF - retro_cjac_2678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	80.58 %
Parental protein coverage:	99.64 %
Number of stop codons detected:	1
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalMENTENSVDSKSIKNSERKIIHGSKSVDSGISLDSSYKMDYPEMGLCLII-NNKNFHKSTGMASRSGTDV
MENTENSVDSKSIKN.E.KI..GSKS.DSGISLD.S.KMDYP.MGLC.II.NN.NFHKSTGMAS.SGTDV
RetrocopyMENTENSVDSKSIKNLEPKIRQGSKSMDSGISLDNSCKMDYPQMGLC-II<NNENFHKSTGMASQSGTDV
ParentalDAANLRETFMNLKYEVRNKNDLTREEIVELMRNVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKI
D.ANLRETFM.LK.EVRNKNDLT.EEIVELM.NVS.E..SKRSSF.CVL.SHGEE.IIFGTNGP.DLKKI
RetrocopyDVANLRETFMKLKDEVRNKNDLTHEEIVELMCNVSEEGDSKRSSFACVLPSHGEEEIIFGTNGPIDLKKI
ParentalTSFFRGDCCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACHKIPVEADFLYAYSTAPGYYSWRNS
.SFFRGDCCRSLTGKPK.F.IQAC.G.ELDCGIE.DSGVDD.M..HK.PVEAD.L.A.STAPGY.SW.NS
RetrocopyASFFRGDCCRSLTGKPKFFLIQACHGIELDCGIEIDSGVDDGMVRHKTPVEADLLHAHSTAPGYHSW*NS
ParentalRDGSWFIQSLCAMLKLYANKLEFMHILTRVNR-KVATEFESSSFDATFHAKKQIPCIVSMLTKELYFY
.DGSWFIQSLCAML...A.KL.FMH....VN..KVATEFES.S.DATF.AKKQIPCIVSMLTKELYFY
RetrocopyKDGSWFIQSLCAMLEQCAHKLAFMH---KVNQ<KVATEFESFSLDATFNAKKQIPCIVSMLTKELYFY

                            

                            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	0 .00 RPM	14 .20 RPM
SRP051959_heart	0 .00 RPM	9 .45 RPM
SRP051959_kidney	0 .00 RPM	10 .69 RPM
SRP051959_liver	0 .00 RPM	10 .09 RPM
SRP051959_lung	0 .00 RPM	25 .91 RPM
SRP051959_lymph_node	0 .00 RPM	48 .99 RPM
SRP051959_skeletal_muscle	0 .00 RPM	9 .67 RPM
SRP051959_spleen	0 .00 RPM	19 .71 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_2678 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2678 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cjac_2678 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005740	2 retrocopies	retro_cjac_2678 , retro_cjac_3011,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Dipodomys ordii	ENSDORG00000002554	2 retrocopies	retro_dord_178, retro_dord_620,
Homo sapiens	ENSG00000164305	1 retrocopy	retro_hsap_406,
Gorilla gorilla	ENSGGOG00000025155	1 retrocopy	retro_ggor_402,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Nomascus leucogenys	ENSNLEG00000010895	1 retrocopy	retro_nleu_1005,
Pongo abelii	ENSPPYG00000015236	1 retrocopy	retro_pabe_312,
Pan troglodytes	ENSPTRG00000016640	1 retrocopy	retro_ptro_310,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,

	RetrogeneDB ID:	retro_cjac_2678
Retrocopy location	Organism:	*Marmoset (Callithrix jacchus)*
	Coordinates:	5:149974103..149974917(-)
	Located in intron of:	ENSCJAG00000018140
Retrocopy information	Ensembl ID:	ENSCJAG00000035101
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	CASP3
	Ensembl ID:	ENSCJAG00000005740
	Aliases:	None
	Description:	caspase 3, apoptosis-related cysteine peptidase [Source:HGNC Symbol;Acc:1504]

Parental	MENTENSVDSKSIKNSERKIIHGSKSVDSGISLDSSYKMDYPEMGLCLII-NNKNFHKSTGMASRSGTDV
	MENTENSVDSKSIKN.E.KI..GSKS.DSGISLD.S.KMDYP.MGLC.II.NN.NFHKSTGMAS.SGTDV
Retrocopy	MENTENSVDSKSIKNLEPKIRQGSKSMDSGISLDNSCKMDYPQMGLC-II<NNENFHKSTGMASQSGTDV

Parental	DAANLRETFMNLKYEVRNKNDLTREEIVELMRNVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKI
	D.ANLRETFM.LK.EVRNKNDLT.EEIVELM.NVS.E..SKRSSF.CVL.SHGEE.IIFGTNGP.DLKKI
Retrocopy	DVANLRETFMKLKDEVRNKNDLTHEEIVELMCNVSEEGDSKRSSFACVLPSHGEEEIIFGTNGPIDLKKI

Parental	TSFFRGDCCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACHKIPVEADFLYAYSTAPGYYSWRNS
	.SFFRGDCCRSLTGKPK.F.IQAC.G.ELDCGIE.DSGVDD.M..HK.PVEAD.L.A.STAPGY.SW.NS
Retrocopy	ASFFRGDCCRSLTGKPKFFLIQACHGIELDCGIEIDSGVDDGMVRHKTPVEADLLHAHSTAPGYHSW*NS

Parental	RDGSWFIQSLCAMLKLYANKLEFMHILTRVNR-KVATEFESSSFDATFHAKKQIPCIVSMLTKELYFY
	.DGSWFIQSLCAML...A.KL.FMH....VN..KVATEFES.S.DATF.AKKQIPCIVSMLTKELYFY
Retrocopy	KDGSWFIQSLCAMLEQCAHKLAFMH---KVNQ<KVATEFESFSLDATFNAKKQIPCIVSMLTKELYFY

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

RetrogeneDB ID:

retro_cjac_2678