RetrogeneDB ID:

retro_ptro_733

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:12:8371714..8372789(-)
Located in intron of:ENSPTRG00000004631
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:POU5F1
Ensembl ID:ENSPTRG00000017953
Aliases:POU5F1, OTF-3, oct-3
Description:Pan troglodytes POU class 5 homeobox 1 (POU5F1), mRNA. [Source:RefSeq mRNA;Acc:NM_001252041]


Retrocopy-Parental alignment summary:






>retro_ptro_733
ATGGCGGGACACCTGGCTTCGGATTTCGCCTTCTCACCCCCTCCAGGCGGTGGAGGTGATGGGCCAGGGGGGCCGGAGCC
GGGCTGGGTTGATCCTCGGACCTGGCTAAGCTTCCAAGGCCCTCCTGGAGGGCCAGGAATCGGGCCGGGGTTTGGGCCAG
GCTCTGAGGAGTGGGGGATTCCCCCATGTCCCCCGCCGTATGAGTTCTGCGGGGGGATGGCGTACTGTGGGCCTCAGACT
GGAGTGGGGCTAGTGCCCCAAGGCGGCTTGGAGACCTCTCAGCCTGAGGGCGAAGCAGGAGTCGGGGTGGAGAGCAACTC
CGATGGGGCCTCCCCGGAGCCCTGCACCGTCTCCCCTGGTGCCGTGAAGCTGGAGAAGAAGCTGGAGCAAAACCCGGAGG
AGTCCCAGGACATCAAAGCTCTGCAGAAAGAACTCGAGCAATTTGCCAAGCTCCTGAAGCAGAAGGGGATCACCCTGGGA
TATACACAGGCCGATGTGGCTCACCCTGGGGGTTCTATTTGGGAAGGTGTTCAGCCAAACGACCATCTGCCGCTTTGAGG
CTCTGCAGGTTAGCTTCAAGAACATGCGTGAGCTGCGGCCCTTGCTGCAGAAGTGGGTGGAGGAAGCTGACAACAATGAA
AATCATCAGGAGATATGCAAAGCAGAAACCCTCGTGCAGGCCCGAAAGAGAAAGCGAACCAGTATCGAGAACCGAGTGAG
AGGCAACCTGGAGAATTTGTTCCAGCGGTGCCCAAAACCCACACTGCAGCAGATCAGCCACATCGCCCAGCAGCTTGGGC
TGGAGAAGGATGTGGTCCGAGTGTGGTTCTGTAACCGGCGCCAGAAGGGCAAGCGATCAAGCAGTGGCTATGCACAACGA
GAGCATTTTGAGGCTGTTGGGTCTCCTTTCTCAGGGGGACCAGTGTCCTTTCCTCTGGCCCCAGGGCCCCATTTTGGTAC
CCCAGGCTATGGGAGCCCTCACTTCACTGCACTGTACTCCTCGGTCCCTTTCCCTGAGGGGGAAGCCTTTCCCCCTGTCT
CCATCACCACTCTGGGCTCTCCCATGCATTCAAAC

ORF - retro_ptro_733 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.37 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAGHLASDFAFSPPPGGGGDGPGGPEPGWVDPRTWLSFQGPPGGPGIGPGVGPGSEVWGIPPCPPPYEFC
MAGHLASDFAFSPPPGGGGDGPGGPEPGWVDPRTWLSFQGPPGGPGIGPG.GPGSE.WGIPPCPPPYEFC
RetrocopyMAGHLASDFAFSPPPGGGGDGPGGPEPGWVDPRTWLSFQGPPGGPGIGPGFGPGSEEWGIPPCPPPYEFC
ParentalGGMAYCGPQVGVGLVPQGGLETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLEKEKLEQNPEESQDIK
GGMAYCGPQ.GVGLVPQGGLETSQPEGEAGVGVESNSDGASPEPCTV.PGAVKLEK.KLEQNPEESQDIK
RetrocopyGGMAYCGPQTGVGLVPQGGLETSQPEGEAGVGVESNSDGASPEPCTVSPGAVKLEK-KLEQNPEESQDIK
ParentalALQKELEQFAKLLKQKRITLGYTQADV-GLTLGVLFG-KVFSQTTICRFEALQLSFKNMCKLRPLLQKWV
ALQKELEQFAKLLKQK.ITLGYTQADV.G...G...G.KVFSQTTICRFEALQ.SFKNM..LRPLLQKWV
RetrocopyALQKELEQFAKLLKQKGITLGYTQADV<GSPWGFYLG<KVFSQTTICRFEALQVSFKNMRELRPLLQKWV
ParentalEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVRVWF
EEADNNEN.QEICKAETLVQARKRKRTSIENRVRGNLENLF..CPKPTLQQISHIAQQLGLEKDVVRVWF
RetrocopyEEADNNENHQEICKAETLVQARKRKRTSIENRVRGNLENLFQRCPKPTLQQISHIAQQLGLEKDVVRVWF
ParentalCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGYGSPHFTALYSSVPFPEGEAFPPV
CNRRQKGKRSSS.YAQRE.FEA.GSPFSGGPVSFPLAPGPHFGTPGYGSPHFTALYSSVPFPEGEAFPPV
RetrocopyCNRRQKGKRSSSGYAQREHFEAVGSPFSGGPVSFPLAPGPHFGTPGYGSPHFTALYSSVPFPEGEAFPPV
ParentalSVTTLGSPMHSN
S.TTLGSPMHSN
RetrocopySITTLGSPMHSN

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 .36 RPM 1 .05 RPM
SRP007412_cerebellum 0 .72 RPM 0 .79 RPM
SRP007412_heart 0 .09 RPM 0 .15 RPM
SRP007412_kidney 0 .24 RPM 0 .76 RPM
SRP007412_liver 0 .33 RPM 0 .26 RPM
SRP007412_testis 0 .00 RPM 0 .00 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_733 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_733 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_733 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 63 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000103773 retrocopies
retro_amel_1057, retro_amel_1213, retro_amel_1616,
Bos taurus ENSBTAG000000211112 retrocopies
retro_btau_1576, retro_btau_951,
Canis familiaris ENSCAFG000000004851 retrocopy
retro_cfam_1538,
Callithrix jacchus ENSCJAG000000197891 retrocopy
retro_cjac_123,
Dipodomys ordii ENSDORG000000095491 retrocopy
retro_dord_65,
Equus caballus ENSECAG000000089671 retrocopy
retro_ecab_301,
Erinaceus europaeus ENSEEUG000000153572 retrocopies
retro_eeur_196, retro_eeur_558,
Felis catus ENSFCAG000000010783 retrocopies
retro_fcat_1372, retro_fcat_1422, retro_fcat_275,
Gorilla gorilla ENSGGOG000000276623 retrocopies
retro_ggor_2275, retro_ggor_295, retro_ggor_852,
Macropus eugenii ENSMEUG000000132213 retrocopies
retro_meug_1146, retro_meug_1475, retro_meug_692,
Microcebus murinus ENSMICG000000015111 retrocopy
retro_mmur_1423,
Myotis lucifugus ENSMLUG000000110283 retrocopies
retro_mluc_1465, retro_mluc_2382, retro_mluc_515,
Mustela putorius furoENSMPUG000000012022 retrocopies
retro_mputfur_253, retro_mputfur_96,
Mus musculus ENSMUSG000000244062 retrocopies
retro_mmus_2201, retro_mmus_250,
Oryctolagus cuniculus ENSOCUG000000171603 retrocopies
retro_ocun_1175, retro_ocun_1696, retro_ocun_463,
Otolemur garnettii ENSOGAG000000006213 retrocopies
retro_ogar_1406, retro_ogar_1436, retro_ogar_2229,
Ochotona princeps ENSOPRG000000039262 retrocopies
retro_opri_1213, retro_opri_556,
Pongo abelii ENSPPYG000000172103 retrocopies
retro_pabe_2761, retro_pabe_3294, retro_pabe_898,
Pan troglodytes ENSPTRG00000017953 5 retrocopies
retro_ptro_1798, retro_ptro_204, retro_ptro_2132, retro_ptro_2721, retro_ptro_733 ,
Pteropus vampyrus ENSPVAG000000073342 retrocopies
retro_pvam_724, retro_pvam_74,
Rattus norvegicus ENSRNOG000000464874 retrocopies
retro_rnor_1474, retro_rnor_2186, retro_rnor_2968, retro_rnor_921,
Sus scrofa ENSSSCG000000013932 retrocopies
retro_sscr_252, retro_sscr_678,
Ictidomys tridecemlineatus ENSSTOG000000261033 retrocopies
retro_itri_1076, retro_itri_1705, retro_itri_951,
Tupaia belangeri ENSTBEG000000130444 retrocopies
retro_tbel_3628, retro_tbel_3718, retro_tbel_3779, retro_tbel_4614,
Tarsius syrichta ENSTSYG000000073404 retrocopies
retro_tsyr_1508, retro_tsyr_1630, retro_tsyr_814, retro_tsyr_817,


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