RetrogeneDB ID:

retro_ptro_2314

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:179296010..179297549(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000017600
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GMCL1
Ensembl ID:ENSPTRG00000012021
Aliases:None
Description:Pan troglodytes germ cell-less, spermatogenesis associated 1 (GMCL1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246396]


Retrocopy-Parental alignment summary:






>retro_ptro_2314
ATGGGATCGTCGAGCAGCCAGGTGCTGGGCCAGCCGAGGCGAGCCCTTGCCCAGCAGGAACAGGGTGCCAGGGCCAGGGG
CTCGGCCCGGAGGCCGGACACTGGAGACGATGCGGCGGGCTGCGGCTTCTGTTACTGCCCGGGCAGTCACAAGCGCAAGC
GGAGCAGCGGGCCCTGCTGCTACTGTCACCCGGACTCGCACAGGGACGAGGATGAGGAGGAGGGGGACAAGCAGCAGCCG
CTCCTCAACACCCCTGCAAGGAAAAAATTAAGGAGTACATCCAAATATATTTATCAAACATTATTTTTGAATGGTGAAAA
CAGTGACATTAAGATTTGTGCTCTAGGAGAAGAATGGCGATTACACAAAATATATTTATGTCAATCTGGCTACTTTTCTA
GTATGTTCAGTGGTTCTTGGAAAGAATCCAGCATGAATATTATTGAACTGGAGATTCCTGACCAGAACATTGATGTAGAG
GCACTGCAGGTTGCGTTTGGTTCACTGTATCGAGATGATGTCTTGATAAAACCCAGTCGAGTTGTTGCCATTTTGGCAGC
AGCTTGTATGCTGCAGCTGGATGGTTTAATACAGCAGTGTGGTGAGACAATGAAGGAAACAATTAGTGTGAAAACTGTAT
GCGGTTATTACACATCAGTAGAGATCTATGGATTAGATTCTGTAAAGAAAAAGTGCCTTGAATGGCTTCTAAACAATTTG
ATGACTCACCAGAATGTTAAACTTTTTAAAGAACTCGGTATAAATGTCATGAAACAGCTCATTGGTTCCTCTAACTTATT
TGTGATGCAAGTGGAGATGGATGTATACACCACTCTAAAAAAGTGGATGTTCCTTCAACTTGTGCCTTCTTGGAATGGAT
CTTTAAAACAGCTTTTGACAGAAGCAGATGTCTGGTGTTCTAAACAGAGAAAAGATTTTGAAGGTATGGCCTTTCTTGAA
ACTGAACCAGGAAAACCGTTTGTGTCAGTATTCAGACATTTAAGGTTACAATATATTATCAGTGACCTAGCTTCTGCAAG
AATTATTGAACAAGATGCTATAGTACCTTCAGAATGGCTGTCTTCTGTGTATAAACAGCAGTGGTTTGCTATGCTGCGGG
CAGAACAAGACCGTGAGGTAGGGCCTCAAGAAATCAATAAAGAAGACCTAGAGGGAAATAGCATGAGGTGTGGTAGAAAG
CTTGCCAAAGATGGTGAATACTGCTGGTGTTGGACGGGTTTTAACTTCGGCTTTGACCTACTTGTAATTTACACCAATGG
ATACATCATTTTCAAACGCAATACACTGAATCAGCCAGGCAGCGGGTCTGTCAGTTTACGGCCTCGAAGGAGCATAGCAT
TTAGATTACGCTTGGCTTCTTTTGACAGTAGTGGAAAACTAGTATGTAGTAGAACAACTGGCTATCAAATACTTATACTT
AAAAAGGATCAGGAACAAGTGGTGATGAACTTGGACAGCAGGTTTCTGACCTTCCCTTTATATATCTGCTGTAACTTCTT
GTATATATCACCAGAAAAA

ORF - retro_ptro_2314 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.62 %
Parental protein coverage: 99.61 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGSLSSRVLRQPRPALAQQAQGARAGGSARRPDTGDDAAGHGFCYCAGSHKRKRSRGSFCYCHPDSETDE
MGS.SS.VL.QPR.ALAQQ.QGARA.GSARRPDTGDDAAG.GFCYC.GSHKRKRS.G..CYCHPDS..DE
RetrocopyMGSSSSQVLGQPRRALAQQEQGARARGSARRPDTGDDAAGCGFCYCPGSHKRKRSSGPCCYCHPDSHRDE
ParentalDEEEGDEQQRLLNTPRRKKLKSTSKYIYQTLFLNGENSDIKICALGEEWSLHKIYLCQSGYFSSMFSGSW
DEEEGD.QQ.LLNTP.RKKL.STSKYIYQTLFLNGENSDIKICALGEEW.LHKIYLCQSGYFSSMFSGSW
RetrocopyDEEEGDKQQPLLNTPARKKLRSTSKYIYQTLFLNGENSDIKICALGEEWRLHKIYLCQSGYFSSMFSGSW
ParentalKESSMNIIELEIPDQNIDVEALQVAFGSLYRDDVLIKPSRVVAILAAACLLQLDGLIQQCGETMKETVNV
KESSMNIIELEIPDQNIDVEALQVAFGSLYRDDVLIKPSRVVAILAAAC.LQLDGLIQQCGETMKET..V
RetrocopyKESSMNIIELEIPDQNIDVEALQVAFGSLYRDDVLIKPSRVVAILAAACMLQLDGLIQQCGETMKETISV
ParentalKTVCGYYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVELFKELSINVMKQLIGSSNLFVMQVEMDIYTALK
KTVCGYYTS...YGLDSVKKKCLEWLLNNLMTHQNV.LFKEL.INVMKQLIGSSNLFVMQVEMD.YT.LK
RetrocopyKTVCGYYTSVEIYGLDSVKKKCLEWLLNNLMTHQNVKLFKELGINVMKQLIGSSNLFVMQVEMDVYTTLK
ParentalKWMFLQLVPSWNGSLKQLLTETDVWFSKQRKDFEGMAFLETEQGKPFVSVFRHLRLQYIISDLASARIIE
KWMFLQLVPSWNGSLKQLLTE.DVW.SKQRKDFEGMAFLETE.GKPFVSVFRHLRLQYIISDLASARIIE
RetrocopyKWMFLQLVPSWNGSLKQLLTEADVWCSKQRKDFEGMAFLETEPGKPFVSVFRHLRLQYIISDLASARIIE
ParentalQDAIVPSEWLSSVYKQQWFAMLRAEQDSEVGPQEINKEELEGNSMRCGRKLAKDGEYCWRWTGFNFGFDL
QDAIVPSEWLSSVYKQQWFAMLRAEQD.EVGPQEINKE.LEGNSMRCGRKLAKDGEYCW.WTGFNFGFDL
RetrocopyQDAIVPSEWLSSVYKQQWFAMLRAEQDREVGPQEINKEDLEGNSMRCGRKLAKDGEYCWCWTGFNFGFDL
ParentalLVTYTNRYIIFKRNTLNQPCSGSVSLQPRRSIAFRLRLASFDSSGKLICSRTTGYQILTLEKDQEQVVMN
LV.YTN.YIIFKRNTLNQP.SGSVSL.PRRSIAFRLRLASFDSSGKL.CSRTTGYQIL.L.KDQEQVVMN
RetrocopyLVIYTNGYIIFKRNTLNQPGSGSVSLRPRRSIAFRLRLASFDSSGKLVCSRTTGYQILILKKDQEQVVMN
ParentalLDSRLLIFPLYICCNFLYISPEK
LDSR.L.FPLYICCNFLYISPEK
RetrocopyLDSRFLTFPLYICCNFLYISPEK

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 5 .83 RPM
SRP007412_cerebellum 0 .00 RPM 8 .57 RPM
SRP007412_heart 0 .00 RPM 3 .58 RPM
SRP007412_kidney 0 .03 RPM 12 .34 RPM
SRP007412_liver 0 .00 RPM 7 .43 RPM
SRP007412_testis 53 .11 RPM 54 .38 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_2314 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2314 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2314 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3407
Pongo abelii retro_pabe_209
Macaca mulatta retro_mmul_98
Parental genes homology:
Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161161 retrocopy
retro_amel_1915,
Choloepus hoffmanni ENSCHOG000000123062 retrocopies
retro_chof_1562, retro_chof_802,
Equus caballus ENSECAG000000168132 retrocopies
retro_ecab_1109, retro_ecab_899,
Homo sapiens ENSG000000873381 retrocopy
retro_hsap_3407,
Loxodonta africana ENSLAFG000000025653 retrocopies
retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus ENSMLUG000000091832 retrocopies
retro_mluc_1521, retro_mluc_31,
Macaca mulatta ENSMMUG000000008581 retrocopy
retro_mmul_98,
Mus musculus ENSMUSG000000011571 retrocopy
retro_mmus_3665,
Nomascus leucogenys ENSNLEG000000101321 retrocopy
retro_nleu_2993,
Oryctolagus cuniculus ENSOCUG000000158082 retrocopies
retro_ocun_112, retro_ocun_160,
Otolemur garnettii ENSOGAG000000084081 retrocopy
retro_ogar_151,
Pongo abelii ENSPPYG000000123341 retrocopy
retro_pabe_209,
Pan troglodytes ENSPTRG00000012021 1 retrocopy
retro_ptro_2314 ,
Pteropus vampyrus ENSPVAG000000012423 retrocopies
retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus ENSSARG000000046511 retrocopy
retro_sara_425,
Sus scrofa ENSSSCG000000083351 retrocopy
retro_sscr_62,
Ictidomys tridecemlineatus ENSSTOG000000007141 retrocopy
retro_itri_59,
Tursiops truncatus ENSTTRG000000074933 retrocopies
retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos ENSVPAG000000017561 retrocopy
retro_vpac_617,


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