RetrogeneDB ID:

retro_ggor_1298

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:17:40924322..40925642(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMC1
Ensembl ID:ENSGGOG00000010620
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ggor_1298
CTGGGTCAAAGTCAGGGTGATGGTCATGGTCCTAGACATGGCAAGAAGGATGACAAGGACAAGAAAAATAAGTACTAACC
TCCTGTACCAACTAGAGTGGCGGAAAAAGAAGAAAAAAACAAAGGGACAAGATGTTGCCAGTAAACTGCCACTGGTGACA
CTTCACACTCAGTGTCGGTTAAAATTACTGAAGTTAGAGAGAATTAAAGACTATCTTCTCATGGAGGAAGAATTCATTAG
AAATCAGGAACAAATAAAACTATTAGAAGAAAAGCAAGAGGAGGGAACATCAAAAGTGGATGATCTGAGGGGGACCCCAA
TGTCAGTAGGAAACTTGGAAGAGATCATCGATGACAATCATGCCATTGTGTCTACATCTGTGGGCTCAGAACACTACGAC
AGCATTCTTTCATTTGTAGACAAGGATCTGCTGGAACCTGGCTGCTCGGTTCTGCTCAGACACAAGGTACATGCGGTGAT
AGGGGTGCTGATGGATGACACGGGTCCCCTGGTCACAATGATGAAGGTGGAGAAAGCCCCCCCAGGAGACCTATGCCAAT
ACTGGGGGGTTGGACAACCAAATTCAGGAAATTAAGGAATCTATGGAGCTTCCTCTCCCCCATCCTGAATATTATGAAGA
GATGGATACAAAGCCTCCTAAAGGGGTCATTCTCTGTGGTCCACCTGGCACAGGTAAAAACCTTGTTAGCCAAAGCAGTA
GCAACCAAACCTCAGCCACTTTCTTGAGAGTGGTTGGCTCTGAACTTATTCGGAAGTACCTAGGTGATGGGCCCAAACTC
GTACGGCAATTGTTTCAAGTTGCTGAAGAACATGCACTATCCATCATGTTTACTGATGAAATTGAAGCCATTGGGACAAA
AAGATATGACTCCAATTCTGGTGGTGAGAGAGAAATTCAGCAAACAATGTTGGAATTGGAACTGTTGAACCAATTGGGTG
GATTTGATTCTGGGAAGATGTGAAAGTTATCATGGCCACAAAATAAATAGAAACTTTGGATCCAGTACTTATCAGACCAG
GCCGCATTGACAAGAAGATCGAGTTCCACCCGCCTGATGAAAAGACTAAGAAGCACATCTTTCAGATTCACACAAGCAGG
ATGACACTGGCCAATGATGTAACCCTGGACGACTTGATCATGGCTAAAGATGACTTCTCTGGTGCTGACATCAAGGCAAT
CTGTACAGAAGCTGGTCTGATGGCCTTAAGAAACATAGAATGAAAGCAACAAATGAAGACTTCAAAAAATCTAAAGAAAG
TGTTCTTTATAAGAAACACGAAGGCATCCCTGAAGGGCTT

ORF - retro_ggor_1298 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.36 %
Parental protein coverage: 99.55 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVG-KKKKKTKGPDAASKLPLVTPHTQCRLKLLKLERIK
.GQSQ..GHGP..GKKDDKDKK.KY.PPVPTRV..KKKKKTKG.D.ASKLPLVT.HTQCRLKLLKLERIK
RetrocopyLGQSQGDGHGPRHGKKDDKDKKNKY*PPVPTRVA>KKKKKTKGQDVASKLPLVTLHTQCRLKLLKLERIK
ParentalDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHYVSILSFV
DYLLMEEEFIRNQEQ.K.LEEKQEE..SKVDDLRGTPMSVG.LEEIIDDNHAIVSTSVGSEHY.SILSFV
RetrocopyDYLLMEEEFIRNQEQIKLLEEKQEEGTSKVDDLRGTPMSVGNLEEIIDDNHAIVSTSVGSEHYDSILSFV
ParentalDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKA-PQETYADIGGLDNQIQEIKESVELPLTHP
DKDLLEPGCSVLL.HKVHAVIGVLMDDT.PLVT.MKVEKA.PQETYA..GGLDNQIQEIKES.ELPL.HP
RetrocopyDKDLLEPGCSVLLRHKVHAVIGVLMDDTGPLVTMMKVEKA>PQETYANTGGLDNQIQEIKESMELPLPHP
ParentalEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHA
EYYEEM..KPPKGVIL.GPPGTGK.L......NQTSATFLRVVGSELI.KYLGDGPKLVR.LF.VAEEHA
RetrocopyEYYEEMDTKPPKGVILCGPPGTGKNLVSQSSSNQTSATFLRVVGSELIRKYLGDGPKLVRQLFQVAEEHA
ParentalPSIVFIDEIDAIGTKRYDSNSGGEREIQRTM--LELLNQLDGFDSR-GDVKVIMATNRIETLDPALIRPG
.SI.F.DEI.AIGTKRYDSNSGGEREIQ.TM..LELLNQL.GFDS...DVKVIMAT..IETLDP.LIRPG
RetrocopyLSIMFTDEIEAIGTKRYDSNSGGEREIQQTMLELELLNQLGGFDSG<EDVKVIMATK*IETLDPVLIRPG
ParentalRIDRKIEFPLPDEKTKKHIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALR-ERRMKV
RID.KIEF..PDEKTKKHIFQIHTSRMTLA.DVTLDDLIMAKDD.SGADIKAICTEAGLMALR...RMK.
RetrocopyRIDKKIEFHPPDEKTKKHIFQIHTSRMTLANDVTLDDLIMAKDDFSGADIKAICTEAGLMALR<KHRMKA
ParentalTNEDFKKSKENVLYKKQEGTPEGL
TNEDFKKSKE.VLYKK.EG.PEGL
RetrocopyTNEDFKKSKESVLYKKHEGIPEGL

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 84 .11 RPM
SRP007412_cerebellum 0 .00 RPM 52 .64 RPM
SRP007412_heart 0 .00 RPM 38 .62 RPM
SRP007412_kidney 0 .00 RPM 73 .60 RPM
SRP007412_liver 0 .00 RPM 41 .78 RPM
SRP007412_testis 0 .00 RPM 111 .47 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_1298 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_1298 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3323
Pan troglodytes retro_ptro_2153
Pongo abelii retro_pabe_2737

Parental genes homology:
Parental genes homology involve 14 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000175102 retrocopies
Choloepus hoffmanni ENSCHOG000000135951 retrocopy
Callithrix jacchus ENSCJAG000000177017 retrocopies
Dasypus novemcinctus ENSDNOG000000064581 retrocopy
Homo sapiens ENSG0000010076410 retrocopies
Gorilla gorilla ENSGGOG00000010620 8 retrocopies
Macropus eugenii ENSMEUG000000015261 retrocopy
Microcebus murinus ENSMICG000000167337 retrocopies
Macaca mulatta ENSMMUG000000229901 retrocopy
Nomascus leucogenys ENSNLEG0000001701310 retrocopies
Oryctolagus cuniculus ENSOCUG000000062314 retrocopies
Otolemur garnettii ENSOGAG000000323432 retrocopies
Pongo abelii ENSPPYG000000259489 retrocopies
Pan troglodytes ENSPTRG000000066239 retrocopies



Copyright © RetrogeneDB 2014-2017