RetrogeneDB ID:

retro_cjac_841

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:11:28191927..28193238(+)
Located in intron of:ENSCJAG00000009288
Retrocopy
information
Ensembl ID:ENSCJAG00000009431
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1G
Ensembl ID:ENSCJAG00000018949
Aliases:None
Description:eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]


Retrocopy-Parental alignment summary:






>retro_cjac_841
ATGGCAGCTGGGACCCTGTACACGTATCCTGAAAACTGGAGGGCCTTCAAGGCCCTCATCGCTGCTCAGTACAGCGGGGC
TCAGGTCCGCGTGCTCTCCGCACCACCCCACTTCCTCTTTGGCCAAACCAACCGCACCCCTGAATTTCTCCGCAAATTTT
CTGCCGGCAAGGTTCCAGCATTTGAGGGTGACGACGGATTCTGTGTGTTTGAGAGCAATGCCATTGCCTACTATATGAGC
AATGAGGAGCTGCGGGGAAGTACTCCAGAGGTAGCAGCCCAGGTGGTGCAGTGGGTGAGCTTTGCTGATAGCGACATAGT
ACCTCCAGCCAGTACCTGGGTGTTCCCCACCTTGGGCATCATGCACCACAACAAACAGGCCACTGAGAATGCAAAGGAGG
AAGTGAGGCGAATTCTGGGGCTGCTGGATGCTCACTTGAAGATGAGGACTTTTCTGGTGGGCGAACGAGTGACATTGGCT
GACATCACAGTTGTCTGCACTTTGTTGTGGCTTTATAAACAGGTCCTAGAGCCTTCTTTTCGCCAGGCCTGTCCCAGTAC
CAACCGCTGGTTCCTCACCTGCATTAACCAGCCCCAGTTCTGGGCTGTCTTGGGGGAAGTGAAACTGTGTGAGAAGATGG
CCCAGTCTGATGCTAAAAAGTTTGCGGAGAGCCAACCTAAAAGGGACACACCACGGAAAGAGAAGGGTTCGTGGGAAGAG
AAGCAGAAGCCCCAGGCCGAGCGGAAGGAGGAGAAAAAGGCAGCTGCCCCTGCTCCTGAGGAGGAGATGGATGAATGTGA
GCAGGTGCTGGCTGCTGAGCCCAAGGCCAAAGACCCCTTTGCTCACCTGCCCAAAAGTATCTTTGTGTTGGATGAATTTA
AGCCCAAGTACTCCAATGAGGACACACTCCCTGTGGCACTGCCGTATTTCTGGGAGCACTTTGATAAGGACGGCTGGTCC
CTGTGGTACTCAGAGTATCGCTTCCCTGAAGAACTCACTCAGTCCTTCATGAGCTGCAGTCTCATCACTGGAATGTTCCA
GCGACTGGACAAGCTGAGGAAGAATGCCTTCACCAGTGTCATCCTCTTTGGAACCAACAATAGTAGCTCCATTTCTGGAG
TCTGTCTCTTCCGAGGCCAGGAGCTTGCCTTTCCGCTGAGTCCAGATTGGCAGGTGGACTACGAGTCATACACGTGGCGG
AAACTGGATCCTGGCAGCGAGGAGGCCCAGATGCTGGTTCAAGAGTACTTCTCCTGGGAGGGGGCCTTCCAGCATGTGGG
CAAAGCCTTCAATCAGGGCAAGATCTTCAAG

ORF - retro_cjac_841 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.19 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHF.FGQTNRTPEFLRKF.AGKVPAFEGDDGFCVF
RetrocopyMAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFLFGQTNRTPEFLRKFSAGKVPAFEGDDGFCVF
ParentalESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
ESNAIAYY.SNEELRGSTPE.AAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
RetrocopyESNAIAYYMSNEELRGSTPEVAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
ParentalLLDAHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLC
LLDAHLK.RTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQA.P.TNRWFLTCINQPQF.AVLGEVKLC
RetrocopyLLDAHLKMRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQACPSTNRWFLTCINQPQFWAVLGEVKLC
ParentalEKMAQFDAKKFAESQPKRDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPF
EKMAQ.DAKKFAESQPKRDTPRKEKGS.EEKQKPQAERKEEKKAAAPAPEEEMDECEQ.LAAEPKAKDPF
RetrocopyEKMAQSDAKKFAESQPKRDTPRKEKGSWEEKQKPQAERKEEKKAAAPAPEEEMDECEQVLAAEPKAKDPF
ParentalAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRLD
AHLPKS.FVLDEFK.KYSNEDTL.VALPYFWEHFDKDGWSLWYSEYRFPEELTQ.FMSC.LITGMFQRLD
RetrocopyAHLPKSIFVLDEFKPKYSNEDTLPVALPYFWEHFDKDGWSLWYSEYRFPEELTQSFMSCSLITGMFQRLD
ParentalKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEEAQTLVREYFSWE
KLRKNAF.SVILFGTNNSSSISGV..FRGQELAFPLSPDWQVDYESYTWRKLDPGSEEAQ.LV.EYFSWE
RetrocopyKLRKNAFTSVILFGTNNSSSISGVCLFRGQELAFPLSPDWQVDYESYTWRKLDPGSEEAQMLVQEYFSWE
ParentalGAFQHVGKAFNQGKIFK
GAFQHVGKAFNQGKIFK
RetrocopyGAFQHVGKAFNQGKIFK

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 1 .44 RPM 266 .83 RPM
SRP051959_heart 1 .53 RPM 225 .85 RPM
SRP051959_kidney 1 .33 RPM 205 .91 RPM
SRP051959_liver 0 .56 RPM 203 .24 RPM
SRP051959_lung 1 .35 RPM 189 .37 RPM
SRP051959_lymph_node 1 .80 RPM 312 .64 RPM
SRP051959_skeletal_muscle 1 .20 RPM 248 .58 RPM
SRP051959_spleen 1 .26 RPM 287 .10 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_841 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_841 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_841 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 21 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000067451 retrocopy
Bos taurus ENSBTAG000000118431 retrocopy
Canis familiaris ENSCAFG000000158346 retrocopies
Callithrix jacchus ENSCJAG00000018949 6 retrocopies
Equus caballus ENSECAG000000143341 retrocopy
Latimeria chalumnae ENSLACG000000147001 retrocopy
Loxodonta africana ENSLAFG000000033391 retrocopy
Myotis lucifugus ENSMLUG000000003421 retrocopy
Monodelphis domestica ENSMODG000000076911 retrocopy
Mustela putorius furoENSMPUG000000139422 retrocopies
Nomascus leucogenys ENSNLEG000000035282 retrocopies
Oryctolagus cuniculus ENSOCUG000000209593 retrocopies
Otolemur garnettii ENSOGAG000000008271 retrocopy
Ochotona princeps ENSOPRG000000145631 retrocopy
Pongo abelii ENSPPYG000000294345 retrocopies
Pan troglodytes ENSPTRG000000037683 retrocopies
Pteropus vampyrus ENSPVAG000000034401 retrocopy
Rattus norvegicus ENSRNOG000000200758 retrocopies
Sorex araneus ENSSARG000000112321 retrocopy
Sus scrofa ENSSSCG000000130641 retrocopy
Tursiops truncatus ENSTTRG000000024593 retrocopies



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