RetrogeneDB ID:

retro_ptro_506

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:10:90689141..90690172(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NUDT9
Ensembl ID:ENSPTRG00000016259
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_506
ATGGCTGGACGCCGCCTGTCCAAGGCTTTAGCGACCGTGTCTCCCTTCATGACCTTGGCCTCTGTGACAGGCAGGCCCGG
CAGCTGCCCCAACATCCTGGCCAGCTGGAGCCTGTTTTCCTCACATAGGTTTTCTCTAAACTTCATCACGTCAGGTTCGA
AGCGCACTGCTGAGAAGCCCCACGAGAAGGCCCGGACATCTCCGTACCCTGGCTCCAAGGTGGAGCGAAGCCTGGTTCCC
CATGAGAAAATGAGCTGGCTGGTCGAGTGGCGAGAGTAACGCCCGTGGAGTACATTGCCAGCTCTGTCTTGCCTGGGCCT
GTGTGGGCAGACCCTCAAGTGGGTGAAAGGAACTTCTCTCCTAAGTTTAACGAAAAGGGTGGGCATGTGGAGAGAAGGAA
ACAGCATGGCTTGTATGAGATTGAGAAGGGTAGACTTAGAAATCCTGCACCTCGGACAGGACTGGTTGGCCAAGGGCCTT
TGGGGTGTTGGGGCCCCAATCATGCTGTAGATCCCATCTTAACCAGATGGAAAAGGGATAGCAAGGGAAACGAAATTACC
CACCCTATTTCTAGAAAAAATATCCTGCAATTTGTAGCCATCAAAAGGAAGGACTGTGGAGAATAGGCAATCCCAGGGGG
TATGGTGGATCCAGGAGAGAAAATTAGTGCTACATTGAAGAGAGAATTTGGCGAGGAAGCCATGAACTCTTTACAGAAAT
CTAGGAAAGAAATGCAGGAGTTGGAGAGACAATTGCACAAACTCCTCAGTCAGGAACATTTTGTGGTCTCTAAAGGCTAC
GTGGATGATTCTAGAAACACAGATAACTGCTGGATAGAGACAGAGGCTGTGAACTACCGTGATGAAATAATGGACCATCT
TCCTCTGGAAGCTGGCGATGATGCCAAGAAAGTGAAATGGGTGGACATTAATGATAAACTTGAGCTTTATGCCAGCCTCT
CCCAATTTATTCAACTTGTGGCTGAGAAACGAGGTGCCCACTGATGTGAGGATATGTATCCTGATTGCCAG

ORF - retro_ptro_506 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.2 %
Parental protein coverage: 99.43 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMARRLLGKALAAVSLSLALASVTIRSSGCRGIPAFRNSFSSSWFHLNTNVMSGSNGSKENSHNKARTSPY
MA.R.L.KALA.VS....LASVT.R...C..I.A....FSS..F.LN....SGS....E..H.KARTSPY
RetrocopyMAGRRLSKALATVSPFMTLASVTGRPGSCPNILASWSLFSSHRFSLNF-ITSGSKRTAEKPHEKARTSPY
ParentalPGSKVERSQVPNEKVGWLVEWQD-YNPVEYTAVSVLAGPRWADPQISESNFSPKFNEKDGHVERKSKNGL
PGSKVERS.VP.EK..WLVEW.....PVEY.A.SVL.GP.WADPQ..E.NFSPKFNEK.GHVER....GL
RetrocopyPGSKVERSLVPHEKMSWLVEWRE<VTPVEYIASSVLPGPVWADPQVGERNFSPKFNEKGGHVERRKQHGL
ParentalYEIENGRPRNPAGRTGLVGRGLLGRWGPNHAADPIITRWKRDSSGNKIMHPVSGKHILQFVAIKRKDCGE
YEIE.GR.RNPA.RTGLVG.G.LG.WGPNHA.DPI.TRWKRDS.GN.I.HP.S.K.ILQFVAIKRKDCGE
RetrocopyYEIEKGRLRNPAPRTGLVGQGPLGCWGPNHAVDPILTRWKRDSKGNEITHPISRKNILQFVAIKRKDCGE
ParentalWAIPGGMVDPGEKISATLKREFGEEALNSLEKTSAEKREIEEKLHKLFSQDHLVIYKGYVDDPRNTDNAW
.AIPGGMVDPGEKISATLKREFGEEA.NSL.K...E..E.E..LHKL.SQ.H.V..KGYVDD.RNTDN.W
Retrocopy*AIPGGMVDPGEKISATLKREFGEEAMNSLQKSRKEMQELERQLHKLLSQEHFVVSKGYVDDSRNTDNCW
ParentalMETEAVNYHDETGEIMDNLMLEAGDDAGKVKWVDINDKLKLYASHSQFIKLVAEKRDAHWSEDSEADCR
.ETEAVNY.DE...IMD.L.LEAGDDA.KVKWVDINDKL.LYAS.SQFI.LVAEKR.AH..ED...DC.
RetrocopyIETEAVNYRDE---IMDHLPLEAGDDAKKVKWVDINDKLELYASLSQFIQLVAEKRGAH*CEDMYPDCQ

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 .54 RPM 23 .08 RPM
SRP007412_cerebellum 0 .72 RPM 20 .97 RPM
SRP007412_heart 1 .40 RPM 17 .17 RPM
SRP007412_kidney 0 .52 RPM 25 .79 RPM
SRP007412_liver 0 .43 RPM 16 .01 RPM
SRP007412_testis 0 .42 RPM 21 .08 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_506 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_506 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_506 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_709
Gorilla gorilla retro_ggor_602
Pongo abelii retro_pabe_613
Callithrix jacchus retro_cjac_1047
Oryctolagus cuniculus retro_ocun_990
Bos taurus retro_btau_1112
Sus scrofa retro_sscr_447
Canis familiaris retro_cfam_1271
Equus caballus retro_ecab_123
Parental genes homology:
Parental genes homology involve 22 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000032441 retrocopy
retro_amel_612,
Bos taurus ENSBTAG000000113541 retrocopy
retro_btau_1112,
Canis familiaris ENSCAFG000000095291 retrocopy
retro_cfam_1271,
Callithrix jacchus ENSCJAG000000061591 retrocopy
retro_cjac_1047,
Equus caballus ENSECAG000000195561 retrocopy
retro_ecab_123,
Echinops telfairi ENSETEG000000191641 retrocopy
retro_etel_348,
Felis catus ENSFCAG000000033151 retrocopy
retro_fcat_1509,
Homo sapiens ENSG000001705021 retrocopy
retro_hsap_709,
Gorilla gorilla ENSGGOG000000147771 retrocopy
retro_ggor_602,
Loxodonta africana ENSLAFG000000113911 retrocopy
retro_lafr_224,
Macropus eugenii ENSMEUG000000121234 retrocopies
retro_meug_1072, retro_meug_1345, retro_meug_1758, retro_meug_2162,
Monodelphis domestica ENSMODG000000207382 retrocopies
retro_mdom_157, retro_mdom_706,
Mustela putorius furoENSMPUG000000022581 retrocopy
retro_mputfur_585,
Nomascus leucogenys ENSNLEG000000095201 retrocopy
retro_nleu_464,
Oryctolagus cuniculus ENSOCUG000000026702 retrocopies
retro_ocun_1045, retro_ocun_990,
Ochotona princeps ENSOPRG000000040551 retrocopy
retro_opri_1152,
Pongo abelii ENSPPYG000000149141 retrocopy
retro_pabe_613,
Pan troglodytes ENSPTRG00000016259 1 retrocopy
retro_ptro_506 ,
Pteropus vampyrus ENSPVAG000000048291 retrocopy
retro_pvam_475,
Sus scrofa ENSSSCG000000092231 retrocopy
retro_sscr_447,
Tursiops truncatus ENSTTRG000000042071 retrocopy
retro_ttru_1549,
Vicugna pacos ENSVPAG000000040121 retrocopy
retro_vpac_125,


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