RetrogeneDB ID:

retro_cjac_446

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:90687157..90688213(+)
Located in intron of:ENSCJAG00000003268
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000018988
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_446
AACACTGGGGTCATCAATGCTCCTGAGATGATCATAAAGGAATTTATCAATAGCACTTTGAGGGACAAGGCAAATACCTC
TCCCTCTGAGATGTTGCCCATGTCTCTCTGGTCCTTGTCTGTGGCCATCTCCGTTTGTGGTATGATTGGCTCCTTTTACG
TCGGATTCTTTGTCATCCACTTTGGCAGGTGCAATTCAGTGCTTATCATCAGCCTGTTGGCTGTCACTGGTGGCTGCCTC
ATGGGATCGTGTAAAGTAGCTGAGTTGCTTGAAATGCTCATCCTGGGCCGCTTAGTTATTGACCTCTTCTGCAGACTATG
CACAGGTTTTGTGCCCATGTACATGTGGAGAGATCTCACCTACTGCCCTGCAGGGTGCCTTTGGTACTCTAAACCAGCTG
AACATTGTTGGAATTCTGGTGGCCCAGGTCTTTGGTCTGGAATTTCTGGAATTCATCCTTGGGTCTGAAGAGCTGCGGCC
AGTGCTGTTGGGCTTTACCATCCTTACTGCTATCCTACAAAGTGCAGCCCTTCCATTTTGCCCTGAAAGTCCCAGATTTT
TGCTCATTAACAGAAAAGAAGAGGATGCTTAGTAGATCCTCCAGTGGTTGTCGGGCACCCAAGATGTATCCCAAGACATC
CAGGAGATGAGCGATGAGAATGCAAGAATGCCACAAGAAAAGCAAGTCACCGTGCTGGAGCACTTTAGAGTATCCAGCTG
CCGACAGCCCATCATCATTTCCATTGTGCTCCAGCTCTCTCAGCAGCTCTCTGGAATCAATGCTGTGTTCTGTTACTCAA
CAGGAATCTTCAAGGATGCAGGTGTTCAAGAACCCATCTATGCCACCATCGGTGAAGGTGTGGCTAATACTGTCTTCACT
GTCGTTTTCCTGTTTCTGGTGGAAAGGGCAGGAAGAAGGACTCTGCATATGATAGACCTTGGAGGGATGGCTTTTTGTCC
CATACACACGACTGTTTTTTTTAGTTATTAAAGGATGACTGTAATGGGATGAGCTTTGTCTGTATTAGGGCTATCTTGGT
CTTTATTCCCTGGTTT

ORF - retro_cjac_446 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.11 %
Parental protein coverage: 70.62 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalNTGVINAPEMIIKEFVNNTLKNKKNAPPSEMLLTSLWSLSVAIFSVGGMIGSFSVGLFVNRFGRRNSMLI
NTGVINAPEMIIKEF.N.TL..K.N..PSEML..SLWSLSVAI.SV.GMIGSF.VG.FV..FGR.NS.LI
RetrocopyNTGVINAPEMIIKEFINSTLRDKANTSPSEMLPMSLWSLSVAI-SVCGMIGSFYVGFFVIHFGRCNSVLI
ParentalVNLLAVTGGCLMGLCKMAESVEMLILGRLVIGLFCGLCTGFVPMYI-GEISPTALRGAFGTLNQLGIVVG
..LLAVTGGCLMG.CK.AE..EMLILGRLVI.LFC.LCTGFVPMY..GEISPTAL.GAFGTLNQL.IV.G
RetrocopyISLLAVTGGCLMGSCKVAELLEMLILGRLVIDLFCRLCTGFVPMYM>GEISPTALQGAFGTLNQLNIV-G
ParentalILVAQIFG---LEFILGSEVLWPVLLGFTILPAILQSAALPFCPESPRFLLINRKEEENAKQILQRLWGT
ILVAQ.FG...LEFILGSE.L.PVLLGFTIL.AILQSAALPFCPESPRFLLINRKEE..A..ILQ.L.GT
RetrocopyILVAQVFGLEFLEFILGSEELRPVLLGFTILTAILQSAALPFCPESPRFLLINRKEED-A**ILQWLSGT
ParentalQDVSQDIQEMKEESARMSQEKQVTVLELFRVSSYRQPIIISIVLQLSQQLSGINAVFYYSTGIFKDAGVQ
QDVSQDIQEM..E.ARM.QEKQVTVLE.FRVSS.RQPIIISIVLQLSQQLSGINAVF.YSTGIFKDAGVQ
RetrocopyQDVSQDIQEMSDENARMPQEKQVTVLEHFRVSSCRQPIIISIVLQLSQQLSGINAVFCYSTGIFKDAGVQ
ParentalEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMALCSLLMTV-SLLLK-DNYNGMSFVCIGAI
EPIYATIG.GV.NT.FTVV.LFLVERAGRRTLHMI.LGGMA.C....TV..L..K.D..NGMSFVCI.AI
RetrocopyEPIYATIGEGVANTVFTVVFLFLVERAGRRTLHMIDLGGMAFCPIHTTV>FLVIK>DDCNGMSFVCIRAI
ParentalLVFVAFF
LVF...F
RetrocopyLVFIPWF

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






(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 2 .06 RPM 9 .07 RPM
SRP051959_heart 1 .70 RPM 8 .16 RPM
SRP051959_kidney 1 .09 RPM 1 .69 RPM
SRP051959_liver 0 .50 RPM 0 .71 RPM
SRP051959_lung 2 .07 RPM 7 .81 RPM
SRP051959_lymph_node 0 .75 RPM 9 .61 RPM
SRP051959_skeletal_muscle 0 .61 RPM 2 .31 RPM
SRP051959_spleen 1 .68 RPM 5 .25 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_446 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_446 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_446 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000045562 retrocopies
Callithrix jacchus ENSCJAG00000018988 1 retrocopy
retro_cjac_446 ,
Cavia porcellus ENSCPOG000000030741 retrocopy
Cavia porcellus ENSCPOG000000098341 retrocopy
Cavia porcellus ENSCPOG000000112951 retrocopy
Felis catus ENSFCAG000000016251 retrocopy
Homo sapiens ENSG000000598042 retrocopies
Gorilla gorilla ENSGGOG000000168131 retrocopy
Macaca mulatta ENSMMUG000000004392 retrocopies
Nomascus leucogenys ENSNLEG000000269032 retrocopies
Oryctolagus cuniculus ENSOCUG000000085751 retrocopy
Pongo abelii ENSPPYG000000042341 retrocopy
Pongo abelii ENSPPYG000000042351 retrocopy
Pan troglodytes ENSPTRG000000046241 retrocopy
Pan troglodytes ENSPTRG000000046261 retrocopy



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