RetrogeneDB ID:

retro_mmul_888

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:11:90668621..90670172(-)
Located in intron of:ENSMMUG00000003574
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.18552
Ensembl ID:ENSMMUG00000019561
Aliases:None
Description:polypeptide N-acetylgalactosaminyltransferase 12 [Source:RefSeq peptide;Acc:NP_001181506]


Retrocopy-Parental alignment summary:






>retro_mmul_888
CCGCTTTATAAGAAGCCCCCTGCAGATTCCCATGCACCTGGGGAGTGGGGGAAAGCCAGCAAACTCCAACTCAACGAGGG
TGAACTGAAGCAGCAAGAAGAACTCATTGAGAGATATGCCATCAATATTTACCTCAGTGACAGAATTTCCCTGCATCGAC
ACATAGAGGATAAAAGAATGTATGAGTGTAAGTCCCAGAAGTTCAACTATAGGACACTTCCTACCACCTCTGTTATCATT
GCTTTCTATAATGAAGCCTGGTCGACTTTGCTCCGTACTATTCACAGTGTTTTAGAAACTTCTCCTGCGGTCCTTTTGAA
AGAGATCATCTTGGTGGATGACTTGAGTGACAGAGTTTATTTGAAGACGCAACTTGAAAGTTACATCAGCAATCTTGATA
GAGTACGCTTGATTAGGACCAATAAGCGAGAGGGGCTGGTTAGGGCCCGTCTGATTGGGGCCACTTTCGCCACTGGGGAC
GTCCTCACTTTCCTGGATTGTCACTGTGAGTGTAATTCCGGTTGGCTGGAACCGCTTTTGGAAAGGATTGGGAGAGATGA
AACAGCAATTGTGTGTCCTGTTATAGACACAATTGATTGGAATACTTTTGAATTCTATATGCAGACAGGGGAGCCCATGA
TTGGTGGGTTTGACTGGCGTTTAACATTTCAGTGGCATTCTGTCCCCAAACACGAAAGGGACAGGCGGATATCAAGAATT
GACCCCATCAGATCACCCACCATGGCTGGAGGACTGTTTGCTGTCAGCAAGAAATATTTTCAGTACCTGGGAACATATGA
CACAGGAATGGAAGTGTGGGGAGGTGAAAACCTTGAACTGTCTTTTAGGGTGTGGCAGTGTGGTGGCAAATTGGAGATCC
ACCCGTGTTCCCACGTGGGCCATGTGTTCCCCAAGCGGGCACCGTATGCTCGCCCCAATTTCCTACAGAATACTGCTCGG
GTAGCAGAAGTTTGGATGGATGAGTACAAAGAGCACTTCTACAATAGAAACCCTCCAGCAAGAAAAGAAGCTTATGGTGA
TATTTCTGAAAGAAAATTAATACGAGAGCGGCTGAGATGCAAGAGCTTTGACTGGTATTTGAAAAACGTGTTTCCTAATT
TACATGTTCCAGAGGATAGGCCAGGCTGGCATGGGGCTATTCGCAGTAGAGGGATCTCTTCTGAATGTTTAGATTATAAT
TCTCCTGACAACAACCCCACAGGTGCTAACCTTTCACTGTTTGGATGCCATGGTCAAGGAGGCAATCAATTCTTTGAATA
TACTTCAAACAAAGAAATAAGGTTTAATTCTGTGACAGAGTTATGTGCAGAGGTTCCTGAGCAAAAAAATTATGTAGGAA
TGCAAAATTGTCCCAAAGATGGGTTCCTTGTACCAGCAAACATTATTTGGCATTTTAAAGAAGATGGAACTATTTTTCAC
CCACACTCAGGACTGTGTCTTAGTGCTTATCGGACACCGGAGGGCCGACCTGATGTACAAATGAGAACTTGTGATGCTCT
AGATAAAAATCAAATTTGGAGTTTTGAGAAA

ORF - retro_mmul_888 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.85 %
Parental protein coverage: 88.81 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalPVLPRPPVPANALGARGEAVRLQLQGEELRLQEESVRLHQINIYLSDRISLHRRLPERWNPLCKEKKYDY
P....PP....A.G..G.A..LQL...EL..QEE......INIYLSDRISLHR.........CK..K..Y
RetrocopyPLYKKPPADSHAPGEWGKASKLQLNEGELKQQEELIERYAINIYLSDRISLHRHIEDKRMYECKSQKFNY
ParentalDNLPRTSVIIAFYNEAWSTLLRTVYSVLETSPDILLEEVILVDDYSDREHLKERLANELSGLPKVRLIRA
..LP.TSVIIAFYNEAWSTLLRT..SVLETSP..LL.E.ILVDD.SDR..LK..L....S.L..VRLIR.
RetrocopyRTLPTTSVIIAFYNEAWSTLLRTIHSVLETSPAVLLKEIILVDDLSDRVYLKTQLESYISNLDRVRLIRT
ParentalNKREGLVRARLLGASAARGDVLTFLDCHCECHEGWLEPLLQRIHEEESAVVCPVIDVIDWNTFEYLGNSG
NKREGLVRARL.GA..A.GDVLTFLDCHCEC..GWLEPLL.RI...E.A.VCPVID.IDWNTFE.....G
RetrocopyNKREGLVRARLIGATFATGDVLTFLDCHCECNSGWLEPLLERIGRDETAIVCPVIDTIDWNTFEFYMQTG
ParentalEPQIGGFDWRLVFTWHTVPERERIRMRSPVDVIRSPTMAGGLFAVSKKYFEYLGSYDTGMEVWGGENLEF
EP.IGGFDWRL.F.WH.VP..ER.R..S..D.IRSPTMAGGLFAVSKKYF.YLG.YDTGMEVWGGENLE.
RetrocopyEPMIGGFDWRLTFQWHSVPKHERDRRISRIDPIRSPTMAGGLFAVSKKYFQYLGTYDTGMEVWGGENLEL
ParentalSFRIWQCGGVLETHPCSHVGHVFPKQAPYSRNKALANSVRAAEVWMDEFKELYYHRNPHARLEPFGDVTE
SFR.WQCGG.LE.HPCSHVGHVFPK.APY.R...L.N..R.AEVWMDE.KE..Y.RNP.AR.E..GD..E
RetrocopySFRVWQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARVAEVWMDEYKEHFYNRNPPARKEAYGDISE
ParentalRKQLRAKLQCKDFKWFLETVYPELHVPEDRPGFFGMLQNQGLKDYCFDYNPPDENQIVGHQVILYVCHGM
RK..R..L.CK.F.W.L..V.P.LHVPEDRPG..G.....G....C.DYN.PD.N...G....L..CHG.
RetrocopyRKLIRERLRCKSFDWYLKNVFPNLHVPEDRPGWHGAIRSRGISSECLDYNSPDNNP-TGANLSLFGCHGQ
ParentalGHNQFFEYTSQKEIRYNTHQPEGCIAVEAGMDILIMHLCEE---TAPENQKFILQEDGSLFHEQSKKCVQ
G.NQFFEYTS.KEIR.N....E.C..V........M..C.......P.N......EDG..FH..S..C..
RetrocopyGGNQFFEYTSNKEIRFNS-VTELCAEVPEQKNYVGMQNCPKDGFLVPANIIWHFKEDGTIFHPHSGLCLS
ParentalAARKESSDSFVPLLRDCTNSD-HQKWFFKE
A.R.......V...R.C...D..Q.W.F..
RetrocopyAYRTPEGRPDVQ-MRTCDALDKNQIWSFEK

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 3 .92 RPM 10 .31 RPM
SRP007412_brain_prefrontal_cortex 1 .59 RPM 8 .49 RPM
SRP007412_cerebellum 2 .13 RPM 27 .38 RPM
SRP007412_heart 1 .77 RPM 5 .77 RPM
SRP007412_kidney 7 .28 RPM 20 .77 RPM
SRP007412_liver 2 .41 RPM 0 .87 RPM
SRP007412_testis 1 .77 RPM 6 .75 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_888 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_888 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_888 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_777
Gorilla gorilla retro_ggor_890
Pongo abelii retro_pabe_949
Mus musculus retro_mmus_183
Rattus norvegicus retro_rnor_2453
Oryctolagus cuniculus retro_ocun_1260
Bos taurus retro_btau_1410
Equus caballus retro_ecab_52
Parental genes homology:
Parental genes homology involve 33 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000023021 retrocopy
retro_acar_54,
Ailuropoda melanoleuca ENSAMEG000000045201 retrocopy
retro_amel_93,
Anas platyrhynchos ENSAPLG000000121971 retrocopy
retro_apla_8,
Bos taurus ENSBTAG000000090371 retrocopy
retro_btau_1410,
Canis familiaris ENSCAFG000000024941 retrocopy
retro_cfam_683,
Cavia porcellus ENSCPOG000000124181 retrocopy
retro_cpor_1467,
Equus caballus ENSECAG000000165461 retrocopy
retro_ecab_52,
Ficedula albicollis ENSFALG000000051881 retrocopy
retro_falb_8,
Felis catus ENSFCAG000000088311 retrocopy
retro_fcat_126,
Gorilla gorilla ENSGGOG000000057921 retrocopy
retro_ggor_890,
Loxodonta africana ENSLAFG000000220111 retrocopy
retro_lafr_536,
Meleagris gallopavo ENSMGAG000000072441 retrocopy
retro_mgal_1,
Microcebus murinus ENSMICG000000110751 retrocopy
retro_mmur_282,
Myotis lucifugus ENSMLUG000000026301 retrocopy
retro_mluc_804,
Macaca mulatta ENSMMUG00000019561 1 retrocopy
retro_mmul_888 ,
Mustela putorius furoENSMPUG000000065021 retrocopy
retro_mputfur_569,
Mus musculus ENSMUSG000000397741 retrocopy
retro_mmus_183,
Nomascus leucogenys ENSNLEG000000170191 retrocopy
retro_nleu_940,
Oryctolagus cuniculus ENSOCUG000000162211 retrocopy
retro_ocun_1260,
Otolemur garnettii ENSOGAG000000014082 retrocopies
retro_ogar_3253, retro_ogar_717,
Ochotona princeps ENSOPRG000000060292 retrocopies
retro_opri_121, retro_opri_515,
Procavia capensis ENSPCAG000000050681 retrocopy
retro_pcap_63,
Pongo abelii ENSPPYG000000194371 retrocopy
retro_pabe_949,
Pelodiscus sinensis ENSPSIG000000172461 retrocopy
retro_psin_1,
Pan troglodytes ENSPTRG000000211801 retrocopy
retro_ptro_777,
Pteropus vampyrus ENSPVAG000000087741 retrocopy
retro_pvam_1347,
Rattus norvegicus ENSRNOG000000080993 retrocopies
retro_rnor_1084, retro_rnor_1085, retro_rnor_2453,
Sarcophilus harrisii ENSSHAG000000174741 retrocopy
retro_shar_44,
Sus scrofa ENSSSCG000000053791 retrocopy
retro_sscr_32,
Ictidomys tridecemlineatus ENSSTOG000000213061 retrocopy
retro_itri_41,
Tupaia belangeri ENSTBEG000000036271 retrocopy
retro_tbel_2065,
Tarsius syrichta ENSTSYG000000049751 retrocopy
retro_tsyr_386,
Tursiops truncatus ENSTTRG000000108481 retrocopy
retro_ttru_212,


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