RetrogeneDB ID:

retro_ggor_1947

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:3:74623913..74625280(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMD12
Ensembl ID:ENSGGOG00000014761
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ggor_1947
ATGGCAGACGGCCACTTGGAGTGGGCTGACAGGCGCATCTTCAAAATGGAAGTGGACTACAACGCCACGGTAGATCAGTG
CCTACCCGAGTGTGAGAAGCTGGCCAAGGAAGGAAGACTTCAAGAAGTCATGGAAACCCTTCTCTCTTTGGAAAAACAGA
CTCGTACTGCTTCTGATATGGGGTCAACATCCCAAATCTTAGTTGCAGTAGTGAAGATGTGCTATGAGGCTAAATAATGG
GATTTACTTAATGAAAATATTACACTTTTGTCCAAAAGGCGGAGTCAATTAATACAAGCTGTTGCCAAAATGGTTCAGTA
GTACTGTATTTATGTTGAGGAAATCACAGACCTTCCTATCAAACTTCAATTAACTGATACTCTATGAATGGTTACCGAAG
GCAAGATTTATGTTGAAATTGAGTGTGCTTGACTGACTAAAACATTAGCAACTATAAAAGAACAAAATGGTGATGTGAAA
GAGGCAGCCTCCGTTTATAGGAGCTACAGGTGGAAACCTATGGATCAATGCAAAAGAAAGAGCAAGTGGAATTTATTTTG
GAGCAAATGAGGCTCTGCCTAGCTGTAAAGGATTACATTCGAACATAAATCATCAGTAAGAAAATTAACACCAAGTTTTT
CCAGGAAGAAAATACAGCGAAATTAAAGTTGAAGTACGATAATTTAATGACTCAGCTGGATGAACACGAGGGATCCTATT
TATTTATTTGTAAGCACTACAGAGCAATATATAATACTCCCTGTATACAGGCAGAAAGTGAAAAATGGCAGCAGGCTATG
AAGAGTGTTGTACCCTATGTTACCCTGGCTCCTTTTGACAATGAACAGTCAGATTTGGTTCACCGAATAAGTGGTGACAA
GAAGTCAGAAGAAATTCCCAAATACAAGGATCTTCTAAAACTTTTCACCACAATGGAGTTGATGCGTTGGTCCACACTTG
TGGAGGACTATGAAATGGAATTAAGCAAAGGTTCCGTTGGCAGTCCTGCAACTGATGCTTTTGGTTCTACAGAGGAAGGC
GAAAAAAGGTGGAAAGATTTGAGTAACAGAGTTGTTGAACATAATATTAGAATAATGGCCAAGTATTATACTCGGATGAC
AATGAAAAGGATGGTACAGCTTCTGGATCTATCTGTTGATGAGTCCGAAGCCTTTCTCTCAAATCTAGTAGTTAACAAGA
CCATATTTGCTAAAGTAGACAGATTAGCAGGAATTAACAACGTCCAGAGACCCAAGGATCCAAATAATTTATGAAATGAC
TGGTCTCAGAAACTGAACTCATTAATGTCTCTGGTTAACAAAACTACACATCTCATAGCTAAAGAGGAGATGATACATAA
TCTACAA

ORF - retro_ggor_1947 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.06 %
Parental protein coverage: 100. %
Number of stop codons detected: 6
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDMVSTSRILVAV
MADG..E.AD.RI.KMEVDY.ATVDQ.LPEC.KLAKEGRLQEV.ETLLSLEKQTRTASDM.STS.ILVAV
RetrocopyMADGHLEWADRRIFKMEVDYNATVDQCLPECEKLAKEGRLQEVMETLLSLEKQTRTASDMGSTSQILVAV
ParentalVKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTLRMVTEGKIYVEI
VKMCYEAK.WDLLNENI.LLSKRRSQL.QAVAKMVQ..C.YVEEITDLPIKL.L.DTL.MVTEGKIYVEI
RetrocopyVKMCYEAK*WDLLNENITLLSKRRSQLIQAVAKMVQ*YCIYVEEITDLPIKLQLTDTL*MVTEGKIYVEI
ParentalERARLTKTLATIKEQNGDVKEAASILQ-ELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKI
E.A.LTKTLATIKEQNGDVKEAAS....ELQVETYGSM.KKE.VEFILEQMRLCLAVKDYIRT.IISKKI
RetrocopyECA*LTKTLATIKEQNGDVKEAASVYR<ELQVETYGSMQKKEQVEFILEQMRLCLAVKDYIRT*IISKKI
ParentalNTKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPF
NTKFFQEENT.KLKLKY.NLM.QLD.HEGSYL.ICKHYRAIY.TPCIQAESEKWQQA.KSVV.YV.LAPF
RetrocopyNTKFFQEENTAKLKLKYDNLMTQLDEHEGSYLFICKHYRAIYNTPCIQAESEKWQQAMKSVVPYVTLAPF
ParentalDNEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEK
DNEQSDLVHRISGDKK.EEIPKYKDLLKLFTTMELMRWSTLVEDY.MEL.KGS..SPATD.FGSTEEGEK
RetrocopyDNEQSDLVHRISGDKKSEEIPKYKDLLKLFTTMELMRWSTLVEDYEMELSKGSVGSPATDAFGSTEEGEK
ParentalRWKDLKNRVVEHNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPK
RWKDL.NRVVEHNIRIMAKYYTR.TMKRM.QLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGI.N.QRPK
RetrocopyRWKDLSNRVVEHNIRIMAKYYTRMTMKRMVQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGINNVQRPK
ParentalDPNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ
DPNNL.NDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ
RetrocopyDPNNL*NDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 24 .12 RPM
SRP007412_cerebellum 0 .00 RPM 13 .59 RPM
SRP007412_heart 0 .00 RPM 3 .56 RPM
SRP007412_kidney 0 .00 RPM 15 .42 RPM
SRP007412_liver 0 .00 RPM 13 .11 RPM
SRP007412_testis 0 .00 RPM 48 .90 RPM
Gorilla gorilla was not studied using ChIP-Seq data.
Gorilla gorilla was not studied using EST data.
Gorilla gorilla was not studied using FANTOM5 data.
retro_ggor_1947 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_1947 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2801
Pan troglodytes retro_ptro_1898
Callithrix jacchus retro_cjac_1400

Parental genes homology:
Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000086912 retrocopies
Homo sapiens ENSG000001971701 retrocopy
Gorilla gorilla ENSGGOG00000014761 1 retrocopy
retro_ggor_1947 ,
Loxodonta africana ENSLAFG000000108761 retrocopy
Nomascus leucogenys ENSNLEG000000012651 retrocopy
Pongo abelii ENSPPYG000000085651 retrocopy
Pan troglodytes ENSPTRG000000227221 retrocopy
Tupaia belangeri ENSTBEG000000147601 retrocopy
Tarsius syrichta ENSTSYG000000131541 retrocopy



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