RetrogeneDB ID:

retro_ptro_3159

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:X:116313542..116314837(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1G
Ensembl ID:ENSPTRG00000003768
Aliases:None
Description:eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]


Retrocopy-Parental alignment summary:






>retro_ptro_3159
ACCCTGTACACATATCCTGAAAACTGAAGGAACTTCAAGGCCCTCATTGCTGCTCAGCACAGAGGGGCTCAGGTCCGTGT
GCTCTCCGCACCACCCCATTTCCACTTTGGCCAAACCAACCGCACCCCTGAATTTCTCTGCAAATTTCCTGCTGGCAAGA
TTCCAGCATTTGAAGGTGACGATAGATTCTGTGTGTTTGAGAGCAATGCCATTGCCTACTATGTGAGCAATGAGGAGCTG
CAGGGAAGTACTCCAGAGGCAGCAGCCCAAGTGATGCAGTGGGTGAGCTTTGCTGATAGCAGTATAGTGTCCCCAGCCAG
TACCTGGGTGTTCCCCACCTTGGGCATCATGCATCACAACAAACAGGCCACTGAGAATACAAAGGAGGAAGTGAGGCAAA
TTCTGGGGCTGTTGGATGCTCACTTGAAGACAAGGACTTTTCTGGAGGGTGAACGAGTGACATTGACTGACATCACAGTT
GTCTGCACCCTATTGTGGCTCTATAAGCAGGTACTAGAACCTTCTTTCTGCCAGGCCTTTCCCAATACCAACCGCTGGTT
CCTCACCTGCATTAACCAGCCTCAGTTCTGCACTGTCTTGGGGAAAGCAAAACTATGTGAGAAGATGGCCCAGTCTGATG
CTAAAAAGTTTGTGGAAAGCCAGCCTAAAAAGGACACACCACGGGAAGAGAAGCGTTCACGGGAAGAGAAGCAGAAGCCC
CAGGCTGAGCAGGAGGAGAAAAAGGCGGCTGCCCCTACTCCTGAGGAGGAGATGGATGAATGTGAGCAGGCGCTGGCCGC
TGAGCCCAAGGCCAAGGACCCCTTTGCTCACCTGCCCAAGAGTACCTTTGTGTTGGATGAATTGAAGCTCAAGTACTCCA
ATGAGACACACTCTCTGTGGCACTGCCATATTTCTGGGAGCACTTTGATAAGGACGGCTGGTCCCTGTTGTACTCAGAGT
ATCGCTTCCCTGAAGAATTCACTCAGACCTTCATGAGCTGCAATCTCATCACTGGAATGTTCCAGTGACTGGACAAGCTG
AGGAAGAATGCCTTCGCCAGTGTCATCCTCTTTGGAACCAACAATATCAGCTCCATTTCTGGAGTCTGGGTCTTCCGAGG
CCAGGAGCTTGCCTTTCCACTGAGTCCAGATTGGCAGGTGGGCTATGAGTCATACACATGGCAGAAACTGGATCCTGGCA
GCGAGGAGACCCAGATGCTGTTTCGAGAGTACTTTTCCTGGGAGGGGGCCTTCTAGCATGTGGGCAAACCCTTCAATCAG
GGCAAGATCTTCAAG

ORF - retro_ptro_3159 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.32 %
Parental protein coverage: 88.91 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVFESNA
TLYTYPEN.R.FKALIAAQ..GAQVRVLSAPPHFHFGQTNRTPEFL.KFPAGK.PAFEGDD.FCVFESNA
RetrocopyTLYTYPEN*RNFKALIAAQHRGAQVRVLSAPPHFHFGQTNRTPEFLCKFPAGKIPAFEGDDRFCVFESNA
ParentalIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILGLLDA
IAYYVSNEEL.GSTPEAAAQV.QWVSFADS.IV.PASTWVFPTLGIMHHNKQATEN.KEEVR.ILGLLDA
RetrocopyIAYYVSNEELQGSTPEAAAQVMQWVSFADSSIVSPASTWVFPTLGIMHHNKQATENTKEEVRQILGLLDA
ParentalYLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLCEKMA
.LKTRTFL.GERVTL.DITVVCTLLWLYKQVLEPSF.QAFPNTNRWFLTCINQPQF..VLG..KLCEKMA
RetrocopyHLKTRTFLEGERVTLTDITVVCTLLWLYKQVLEPSFCQAFPNTNRWFLTCINQPQFCTVLGKAKLCEKMA
ParentalQFDAKKFAETQPKKDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPFAHLP
Q.DAKKF.E.QPKKDTPR.EK.SREEKQKPQAE..EEKKAAAP.PEEEMDECEQALAAEPKAKDPFAHLP
RetrocopyQSDAKKFVESQPKKDTPREEKRSREEKQKPQAE-QEEKKAAAPTPEEEMDECEQALAAEPKAKDPFAHLP
ParentalKSTFVLDEFKRKYSNE-DTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRLDKLR
KSTFVLDE.K.KYSNE.DTLSVALPYFWEHFDKDGWSL.YSEYRFPEE.TQTFMSCNLITGMFQ.LDKLR
RetrocopyKSTFVLDELKLKYSNE<DTLSVALPYFWEHFDKDGWSLLYSEYRFPEEFTQTFMSCNLITGMFQ*LDKLR
ParentalKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVREYFSWEGAF
KNAFASVILFGTNN.SSISGVWVFRGQELAFPLSPDWQV.YESYTW.KLDPGSEETQ.L.REYFSWEGAF
RetrocopyKNAFASVILFGTNNISSISGVWVFRGQELAFPLSPDWQVGYESYTWQKLDPGSEETQMLFREYFSWEGAF
ParentalQHVGKAFNQGKIFK
.HVGK.FNQGKIFK
Retrocopy*HVGKPFNQGKIFK

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
SRP007412_brain_prefrontal_cortex 0 .02 RPM 195 .55 RPM
SRP007412_cerebellum 0 .07 RPM 228 .07 RPM
SRP007412_heart 0 .03 RPM 290 .06 RPM
SRP007412_kidney 0 .08 RPM 641 .01 RPM
SRP007412_liver 0 .23 RPM 271 .89 RPM
SRP007412_testis 0 .11 RPM 237 .32 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_3159 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_3159 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3159 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4744
Pongo abelii retro_pabe_3690
Parental genes homology:
Parental genes homology involve 26 parental genes, and 69 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 ENSCJAG000000189496 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,
Erinaceus europaeus ENSEEUG000000012311 retrocopy
retro_eeur_575,
Homo sapiens ENSG000002547724 retrocopies
retro_hsap_2778, retro_hsap_2982, retro_hsap_3906, retro_hsap_4744,
Latimeria chalumnae ENSLACG000000147001 retrocopy
retro_lcha_82,
Loxodonta africana ENSLAFG000000033391 retrocopy
retro_lafr_381,
Myotis lucifugus ENSMLUG000000003421 retrocopy
retro_mluc_1110,
Macaca mulatta ENSMMUG000000065985 retrocopies
retro_mmul_1447, retro_mmul_1905, retro_mmul_2528, retro_mmul_736, retro_mmul_802,
Monodelphis domestica ENSMODG000000076911 retrocopy
retro_mdom_68,
Mustela putorius furoENSMPUG000000139422 retrocopies
retro_mputfur_427, retro_mputfur_944,
Mus musculus ENSMUSG000000716447 retrocopies
retro_mmus_1447, retro_mmus_1839, retro_mmus_2350, retro_mmus_2765, retro_mmus_3080, retro_mmus_425, retro_mmus_989,
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 ENSPTRG00000003768 3 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,
Ictidomys tridecemlineatus ENSSTOG000000028512 retrocopies
retro_itri_852, retro_itri_886,
Tursiops truncatus ENSTTRG000000024593 retrocopies
retro_ttru_1082, retro_ttru_1544, retro_ttru_1603,


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