RetrogeneDB ID:

retro_ptro_1780

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:46725899..46726757(+)
Located in intron of:ENSPTRG00000030255
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NRBF2
Ensembl ID:ENSPTRG00000002539
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_1780
ATGGAAGTAATGGAAGGACCCCTCAACCTGGCTCATCAGCAGAGCAGACGAGCCGACCGTTTATTAGCTGCAGGCAAATA
CGAAGAGGCGATTTCTTGTCACAAAAAGGCTGCGGCATATCTTTCTGAAGCCATGAAGCTGACACAATCTGAGCAGGCTC
ATCTTTCACTGGAATTGCAAAGGGATAGCCACATGAAACAGCTCCTCCTCATCCAAGAGAGATGGAAAAGGGCCCAGCGT
GAGGAAAGATTGAAAGCCTAGCAGAACACAGACAAGGATGTAGCTGCCCATCTTCAGGCATCTCACAAACTCTCTGCCGA
GGATGCGGAGGGCCAGAGCCCCCTTTCTCAGAAGTACAGCCCTTCTTCAGAGAAACGCCTGCCTGAGATTCAGGGGATCT
TTGACAGGGATCCAAACACACTACTATATTTACTTCAGCAAAAGAGTGAGCCAGCAGAGCCATGTATTGGAAGCAAAGCC
CCAGAAGATGATAAAACAATTATAGAGGAGTAGGCAACCAAAATTGCAGATTTGAAGAGGCATGTGGAATTCCTTGTGGC
TGAGAATGAAAGATTAAGGAAAGAAAATAACTAAAGGCTGAAAAGGCCAGACTTCTAAAAAGGTCCAGTAGAAAAAGAGC
TGGATGTAGATGCTGATTTTGTAGAAACGTCAGAATTACGGAGCTTGCCGCCACATTCAGAAACTGCTACAGCCTCCTCA
ACCTGGCAGAAGTTTGCAGCAAATGCCGGGAAAGCCAAGGACATTCCAATCCCCAGTCTTCCTCCCTTGGATTTTACATC
TCCAGAACTTCCCCTTATGGATCTCCCTGAGAATATTCTGAAAGGATTTATGAATAAT

ORF - retro_ptro_1780 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.24 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL
MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL
RetrocopyMEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL
ParentalIQERWKRAQREERLKAQQNTDKDAAAHLQTSHKPSAEDAEGQSPLSQKYSPSTEKCLPEIQGIFDRDPDT
IQERWKRAQREERLKA.QNTDKD.AAHLQ.SHK.SAEDAEGQSPLSQKYSPS.EK.LPEIQGIFDRDP.T
RetrocopyIQERWKRAQREERLKA*QNTDKDVAAHLQASHKLSAEDAEGQSPLSQKYSPSSEKRLPEIQGIFDRDPNT
ParentalLLYLLQQKSEPAEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGP
LLYLLQQKSEPAEPCIGSKAP.DDKTIIEE.ATKIADLKRHVEFLVAENERLRKEN...........KGP
RetrocopyLLYLLQQKSEPAEPCIGSKAPEDDKTIIEE*ATKIADLKRHVEFLVAENERLRKEN-N*RLKRPDF*KGP
ParentalIEKELDVDADFVETSELWSLPPHSETATASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSEDI
.EKELDVDADFVETSEL.SLPPHSETATASSTWQKFAAN.GKAKDIPIP.LPPLDF.SPELPLM.L.E.I
RetrocopyVEKELDVDADFVETSELRSLPPHSETATASSTWQKFAANAGKAKDIPIPSLPPLDFTSPELPLMDLPENI
ParentalLKGFMNN
LKGFMNN
RetrocopyLKGFMNN

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 .05 RPM 12 .39 RPM
SRP007412_cerebellum 0 .07 RPM 9 .97 RPM
SRP007412_heart 0 .00 RPM 3 .21 RPM
SRP007412_kidney 0 .03 RPM 10 .41 RPM
SRP007412_liver 0 .03 RPM 31 .20 RPM
SRP007412_testis 0 .53 RPM 13 .38 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1780 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1780 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1780 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2643
Pongo abelii retro_pabe_2327
Macaca mulatta retro_mmul_1523

Parental genes homology:
Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000046483 retrocopies
Homo sapiens ENSG000001485723 retrocopies
Gorilla gorilla ENSGGOG000000130162 retrocopies
Macropus eugenii ENSMEUG000000108493 retrocopies
Macaca mulatta ENSMMUG000000177261 retrocopy
Monodelphis domestica ENSMODG000000171831 retrocopy
Mus musculus ENSMUSG000000750002 retrocopies
Otolemur garnettii ENSOGAG000000058561 retrocopy
Pongo abelii ENSPPYG000000024113 retrocopies
Pan troglodytes ENSPTRG00000002539 3 retrocopies
retro_ptro_1780 , retro_ptro_194, retro_ptro_2715,
Rattus norvegicus ENSRNOG000000006412 retrocopies
Sarcophilus harrisii ENSSHAG000000047441 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000113411 retrocopy



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