RetrogeneDB ID:

retro_cjac_1770

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:34725182..34726493(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000006131
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_1770
ATGGCGGCTGGGACCCTGTACATGTATCCTGAAAACTGGAGGGCCTTCAAGGCCCTCATCGCTGCTCAATACAGCGGGGC
TCAGGTCCGCGTGCTCTCCGCACCACCCCACTTCCACTTTGGCCAAACCAACCGCACCCCTGAATTTCTCCGCAAATTTC
CTGCCGGCAAGGTTCCAGCATTTGAGGGTGACGACGGATTCTGTGTGTTTGAGAGCAATGCCATTGCCTACTATGTGAGC
AATGAGGAGCTGCAGGGAAGTACTCCAGAGGCAGCCGCCCAGGTGGTGCAGTGGGTGAGCTTTGCCGATAGCGACATAGT
ACCTCCAGCCAGTACCTGGGTGTTCCCCACCTTGGGCATCATGCACCACAACAAACAGGCCACTGAGAATGCGAAGGAGG
AAGTGAGGCGAATTCTGGGGCTGCTGGATGCTCACTTGAAGACGAGGACTTTTCTGGTGGGCGAACGAGTGACACTGGCT
GACATCACAGTTGTCTGCACTTTGTTGTGGCTTTATAAACAGGTCCTAGAGCCTTCTTTCCGCCAGGCCTTTCCCAATAC
CAACTGCTGGTTCCTCACCTGCATTAACAAGCCCCAATTCCGGGCTGTCTTGGGGGAAGTGAAACTGTGTGAGAAGATGG
CCCAGTTTGATGCTAAAAAGTTTGCAGAGAGCCAACCTAAAAGGGACACACCACGGAAAGAGAAGGGGTCACGAGAAGAG
AAGCAGAAACCCCAGGCTGAGCGGAAGGAGGAAAAAAAGGCAGCTGCCCCTGCTCCTGAGGAGGAGATGGATGAATGTGA
GCAGGCGCTGGCTGCTGAGCCCAAGGCCAAAGACCCCTTTGCTCACCTGCCCAAAAGTACCTTTGTGTTAGATGAATTTA
AGCGCAAGTACTCCAATGAGGACACTCTGTCTGTGGCACTGCCATATTTCTGGGAGCACTTTGATAAGGACGGCTGGTCC
CTGTGGTACTCAGAGTATCGCTTCCCTGAAGAACTCACTCAGACCTTCATGAGCTGCAATCTCATCACTGGAATGTTCCA
GCGACTGGACAAGCTGAGGAAGAATGCCTTCGCCAGTGTCATCCTCTTTGGAACCAACAATAGTAGCTCAATTTCTGGAG
TCTGGGTCTTCCGAGGCCAGGAGCTTGCCTTTCCGCTGAGTCCAGATTGGCAGGTGGACTAGGAGTCATACACATGGCGG
AAACTGGATCCTGGCAGCGAGGAGGCCCAGACGCTGGTTCGAGAGTACTTCTCCTGGGAGGGGGCCTTCCAGCATGTGGG
CAAAGCCTTCAATCAGGGCAAGATCTTCAAG

ORF - retro_cjac_1770 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.86 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
MAAGTLY.YPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
RetrocopyMAAGTLYMYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
ParentalESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
ESNAIAYYVSNEEL.GSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
RetrocopyESNAIAYYVSNEELQGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
ParentalLLDAHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLC
LLDAHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTN.WFLTCIN.PQFRAVLGEVKLC
RetrocopyLLDAHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNCWFLTCINKPQFRAVLGEVKLC
ParentalEKMAQFDAKKFAESQPKRDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPF
EKMAQFDAKKFAESQPKRDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPF
RetrocopyEKMAQFDAKKFAESQPKRDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPF
ParentalAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRLD
AHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRLD
RetrocopyAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRLD
ParentalKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEEAQTLVREYFSWE
KLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVD.ESYTWRKLDPGSEEAQTLVREYFSWE
RetrocopyKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVD*ESYTWRKLDPGSEEAQTLVREYFSWE
ParentalGAFQHVGKAFNQGKIFK
GAFQHVGKAFNQGKIFK
RetrocopyGAFQHVGKAFNQGKIFK

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 8 .59 RPM 266 .83 RPM
SRP051959_heart 7 .77 RPM 225 .85 RPM
SRP051959_kidney 6 .74 RPM 205 .91 RPM
SRP051959_liver 6 .76 RPM 203 .24 RPM
SRP051959_lung 6 .30 RPM 189 .37 RPM
SRP051959_lymph_node 10 .32 RPM 312 .64 RPM
SRP051959_skeletal_muscle 7 .93 RPM 248 .58 RPM
SRP051959_spleen 8 .76 RPM 287 .10 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_1770 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1770 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1770 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
retro_amel_772,
Bos taurus ENSBTAG000000118431 retrocopy
retro_btau_1600,
Canis familiaris ENSCAFG000000158346 retrocopies
retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus ENSCJAG00000018949 6 retrocopies
retro_cjac_1464, retro_cjac_1770 , retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Equus caballus ENSECAG000000143341 retrocopy
retro_ecab_419,
Latimeria chalumnae ENSLACG000000147001 retrocopy
retro_lcha_82,
Loxodonta africana ENSLAFG000000033391 retrocopy
retro_lafr_381,
Myotis lucifugus ENSMLUG000000003421 retrocopy
retro_mluc_1110,
Monodelphis domestica ENSMODG000000076911 retrocopy
retro_mdom_68,
Mustela putorius furoENSMPUG000000139422 retrocopies
retro_mputfur_427, retro_mputfur_944,
Nomascus leucogenys ENSNLEG000000035282 retrocopies
retro_nleu_1510, retro_nleu_681,
Oryctolagus cuniculus ENSOCUG000000209593 retrocopies
retro_ocun_1693, retro_ocun_369, retro_ocun_693,
Otolemur garnettii ENSOGAG000000008271 retrocopy
retro_ogar_1344,
Ochotona princeps ENSOPRG000000145631 retrocopy
retro_opri_814,
Pongo abelii ENSPPYG000000294345 retrocopies
retro_pabe_2237, retro_pabe_2378, retro_pabe_2409, retro_pabe_2473, retro_pabe_3690,
Pan troglodytes ENSPTRG000000037683 retrocopies
retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Pteropus vampyrus ENSPVAG000000034401 retrocopy
retro_pvam_1239,
Rattus norvegicus ENSRNOG000000200758 retrocopies
retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Sorex araneus ENSSARG000000112321 retrocopy
retro_sara_718,
Sus scrofa ENSSSCG000000130641 retrocopy
retro_sscr_164,
Tursiops truncatus ENSTTRG000000024593 retrocopies
retro_ttru_1082, retro_ttru_1544, retro_ttru_1603,


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