RetrogeneDB ID:

retro_ptro_29

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:X:133585835..133586606(+)
Located in intron of:ENSPTRG00000022281
Retrocopy
information
Ensembl ID:ENSPTRG00000039108
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PRDX3
Ensembl ID:ENSPTRG00000002992
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_29
ATGGCGGCTGCTGTAGGACGGTTGCTCCGAGCGTCGGTTGCCCGACATGCGAGTGCCATTCCTTGGGGCATTTCTGCCAC
TGCAGCCCTCAGGCCTGCTGCATGTGGAAGAACGAGCTTGACAAATTTATTGTGTTCTGGTTCCAGTCAAGCAAAATTAT
TCAGCACCAGTTCCTCATGCCATGCACCTGCTGTCACCCAGCATGCACCCTATTTTAAGGGTACAGCCATTGTCAATGGA
GAGTTCAAAGACCTAAGCCTTGATGACTTTAAGGGGAAATATTTGGTGCTTTTCTTCTATCCTTTGGATTTCACCTTTGT
GTGTCCTACAGAAATTGTTGCTTTTAGTGACAAAGCTAACGAATTTCACGACGTGAACTGTGAAGTTGTCGCAGTCTCAG
TGGATTCCCACTTTAGCCATCTTGCCTGGATAAATACACCAAGAAAGAATGGTGGTTTGGGCCACATGAACATCGCACTC
TTGTCAGACTTAACTAAGCAGATTTCCCGAGACTACAGTGTGCTGTTAGAAGGTTCTGGTCTTGCACTAAGAGGTCTCTT
CATAATTGACCCCAATGGAGTCATCAAGCACTTAAGCGTCAACGATCTCCCAGTGGGCCGAAGCGTGGAAGAAACCCTCC
GCTTGGTGAAGGCGTTCCAGTATGTAGAAACACATGGAGAAGTCTGCCCAGCGAACTGGACACCGGATTCTCCTACGATC
AAGCCAAGTCCAGCTGCTTCCAAAGAGTACTTTCAGAAGGTAAATCAGTAG

ORF - retro_ptro_29 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.83 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAAVGRLLRASVARHVSAIPWGISATAALRPAACGRTSLTNLLCSGSSQAKLFSTSSSCHAPAVTQHAP
MAAAVGRLLRASVARH.SAIPWGISATAALRPAACGRTSLTNLLCSGSSQAKLFSTSSSCHAPAVTQHAP
RetrocopyMAAAVGRLLRASVARHASAIPWGISATAALRPAACGRTSLTNLLCSGSSQAKLFSTSSSCHAPAVTQHAP
ParentalYFKGTAVVNGEFKDLSLDDFKGKYLVLFFYPLDFTFVCPTEIVAFSDKANEFHDVNCEVVAVSVDSHFSH
YFKGTA.VNGEFKDLSLDDFKGKYLVLFFYPLDFTFVCPTEIVAFSDKANEFHDVNCEVVAVSVDSHFSH
RetrocopyYFKGTAIVNGEFKDLSLDDFKGKYLVLFFYPLDFTFVCPTEIVAFSDKANEFHDVNCEVVAVSVDSHFSH
ParentalLAWINTPRKNGGLGHMNIALLSDLTKQISRDYGVLLEGSGLALRGLFIIDPNGVIKHLSVNDLPVGRSVE
LAWINTPRKNGGLGHMNIALLSDLTKQISRDY.VLLEGSGLALRGLFIIDPNGVIKHLSVNDLPVGRSVE
RetrocopyLAWINTPRKNGGLGHMNIALLSDLTKQISRDYSVLLEGSGLALRGLFIIDPNGVIKHLSVNDLPVGRSVE
ParentalETLRLVKAFQYVETHGEVCPANWTPDSPTIKPSPAASKEYFQKVNQ
ETLRLVKAFQYVETHGEVCPANWTPDSPTIKPSPAASKEYFQKVNQ
RetrocopyETLRLVKAFQYVETHGEVCPANWTPDSPTIKPSPAASKEYFQKVNQ

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 1 .27 RPM 31 .85 RPM
SRP007412_cerebellum 0 .04 RPM 7 .03 RPM
SRP007412_heart 0 .20 RPM 37 .13 RPM
SRP007412_kidney 0 .34 RPM 65 .35 RPM
SRP007412_liver 0 .23 RPM 25 .60 RPM
SRP007412_testis 0 .00 RPM 3 .69 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_29 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_29 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_29 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000087311 retrocopy
retro_btau_562,
Canis familiaris ENSCAFG000000121093 retrocopies
retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Callithrix jacchus ENSCJAG000000196363 retrocopies
retro_cjac_1333, retro_cjac_3082, retro_cjac_653,
Ciona savignyi ENSCSAVG000000012091 retrocopy
retro_csav_6,
Dasypus novemcinctus ENSDNOG000000013593 retrocopies
retro_dnov_1052, retro_dnov_2373, retro_dnov_745,
Equus caballus ENSECAG000000170261 retrocopy
retro_ecab_408,
Erinaceus europaeus ENSEEUG000000092991 retrocopy
retro_eeur_238,
Homo sapiens ENSG000001656723 retrocopies
retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla ENSGGOG000000263641 retrocopy
retro_ggor_986,
Macropus eugenii ENSMEUG000000077323 retrocopies
retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus ENSMICG000000076271 retrocopy
retro_mmur_475,
Myotis lucifugus ENSMLUG000000128713 retrocopies
retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta ENSMMUG000000082942 retrocopies
retro_mmul_1307, retro_mmul_1517,
Monodelphis domestica ENSMODG000000092861 retrocopy
retro_mdom_1062,
Mustela putorius furoENSMPUG000000030741 retrocopy
retro_mputfur_1032,
Mus musculus ENSMUSG000000249971 retrocopy
retro_mmus_2443,
Nomascus leucogenys ENSNLEG000000166983 retrocopies
retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus ENSOCUG000000173342 retrocopies
retro_ocun_135, retro_ocun_1434,
Pongo abelii ENSPPYG000000027001 retrocopy
retro_pabe_1906,
Pan troglodytes ENSPTRG000000006751 retrocopy
retro_ptro_2874,
Pan troglodytes ENSPTRG00000002992 1 retrocopy
retro_ptro_29 ,
Pan troglodytes ENSPTRG000000105413 retrocopies
retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Ictidomys tridecemlineatus ENSSTOG000000025372 retrocopies
retro_itri_1098, retro_itri_1753,
Tupaia belangeri ENSTBEG000000110645 retrocopies
retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus ENSTTRG000000108782 retrocopies
retro_ttru_1703, retro_ttru_881,


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