RetrogeneDB ID:

retro_opri_121

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_2464:151581..152725(-)
Located in intron of:ENSOPRG00000003512
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSOPRG00000006029
Aliases:None
Description:UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12) [Source:HGNC Symbol;Acc:19877]


Retrocopy-Parental alignment summary:






>retro_opri_121
TCAGTCATCATCGCCTTCTACAACGAAGCCTGGTTCCACCTTGCTCCGCACCATGCACAGTGTTCTCGAAACTTCCCCCG
CAGTCCTCCTGAAGGAGATCATCCTGGTCGACGACTTGAGCGACAGAGTTTATCTGAAGGCACAGCTGGAAACGTACGTC
AGCAATCTTGAGAGAGTCCGCCTGATCAGGACCAAAAAGCGTGAGGGGTTGGTGAGGGCCCGCCTCATCGGGGCCACTTT
TGCCACCGGCGACGTCCTCACCTTCCTGGACTGCCACTGTGAGTGTAATTTCGGGTGGCTGGAGCCCCTTTTGGAAAGGA
TTGGGGAAGATGAGACGGCCATTGTCTGCCCTGTGATCGACACCATTGATTGGAATACGTTTGAATTCTATATGCAGACG
GGGGAGCCCATGATTGGTGGGTTTGACTGGCGCTTAACGTTCCAGTGGCAATCTGTCCCCAAACAGGAGAGGGAAAGGCG
CAGGTCGAGAACTGACCCCATCCGGTCTCCCACCATGGCCGGAGGGCTGTTTGCTGTGAGCAAGAAGTACTTTCAGTACC
TTGGAACCTACGACACTGGAATGGAGGTGTGGGGTGGTGAGAACCTGGAGCTGTCTTTCCGGGTGTGGCAGTGCGGTGGG
AAACTGGAGATCCACCCGTGTTCTCACGTGGGCCACGTGTTCCCCAAGCGGGCACCTTACGCCCGCCCCAACTTCCTGCA
GAACACAGCTCGGGCAGCGGAAGTGTGGATGGACGGGTACAAAGAGCACTTCTACAACCGAAACCCTCCAGCCAGAAAGG
AAGATTACGGTGACATTTCCGACAGAAAATTACTACGGGAGCGCCTGAAATGCAAGAGCTTCGACTGGTATCTGAAGAAC
GTGTTTTCCAATTTACACGTTCCGGAGGACAGGCCCGGCTGGCACGGGGCTATCCGTAGCAAAGGCATCTCTTCGGAGTG
CCTAGATTACAACGCCCCGGATAACAATCCCACGGGGGCTAACCTTTCACTCTTTGGGTGCCATGGCCAAGGAGGGAACC
AATTCTTTGAATACACTTCGAACAAAGAGATAAGGTTTAATTCTGTGACAGAGTTGTGTGCGGTGGTTCCTGAGAAAAAA
GATAACGTAGGAATGCAAAATTGC

ORF - retro_opri_121 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.19 %
Parental protein coverage: 84.55 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSVIIAFYNEAW-STLLRTVYSVLETSPDVLLEEVILVDDYSDREHLKERLANELSGLPKVRLIRATKREG
SVIIAFYNEAW.STLLRT..SVLETSP.VLL.E.ILVDD.SDR..LK..L....S.L..VRLIR..KREG
RetrocopySVIIAFYNEAW>STLLRTMHSVLETSPAVLLKEIILVDDLSDRVYLKAQLETYVSNLERVRLIRTKKREG
ParentalLVRARLLGASAAKGDVLTFLDCHCECHEGWLEPLLQRIHEKESAVVCPVIDVIDWNTFEYLGNPGEPQIG
LVRARL.GA..A.GDVLTFLDCHCEC..GWLEPLL.RI.E.E.A.VCPVID.IDWNTFE.....GEP.IG
RetrocopyLVRARLIGATFATGDVLTFLDCHCECNFGWLEPLLERIGEDETAIVCPVIDTIDWNTFEFYMQTGEPMIG
ParentalGFDWRLVFTWHVVPERERLRMRSPIDVIRSPTMAGGLFAVSKKYFEYLGSYDTGMEVWGGENLEFSFRIW
GFDWRL.F.W..VP..ER.R.RS..D.IRSPTMAGGLFAVSKKYF.YLG.YDTGMEVWGGENLE.SFR.W
RetrocopyGFDWRLTFQWQSVPKQERERRRSRTDPIRSPTMAGGLFAVSKKYFQYLGTYDTGMEVWGGENLELSFRVW
ParentalQCGGTLETHPCSHVGHVFPKQAPYSRSKALANSVRAAEVWMDEFKEIYYHRNPRARLEPFGDVTERKQLR
QCGG.LE.HPCSHVGHVFPK.APY.R...L.N..RAAEVWMD..KE..Y.RNP.AR.E..GD...RK.LR
RetrocopyQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDGYKEHFYNRNPPARKEDYGDISDRKLLR
ParentalEKLQCKDFKWFLETVYPELHVPEDRPGFFGMLQNKGLKDYCFDYNPPDENQITGHQVILYMCHGMGQNQF
E.L.CK.F.W.L..V...LHVPEDRPG..G....KG....C.DYN.PD.N..TG....L..CHG.G.NQF
RetrocopyERLKCKSFDWYLKNVFSNLHVPEDRPGWHGAIRSKGISSECLDYNAPDNNP-TGANLSLFGCHGQGGNQF
ParentalFEYTSQKEIRYNTHQPEGCVAVEVGKDILVMHPC
FEYTS.KEIR.N....E.C..V...KD...M..C
RetrocopyFEYTSNKEIRFNS-VTELCAVVPEKKDNVGMQNC

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ochotona princeps was not studied using ChIP-Seq data.

EST - click to see more details

Ochotona princeps was not studied using EST data.

TSS - click to see more details

Ochotona princeps was not studied using FANTOM5 data.

Lab - click to see more details

retro_opri_121 was not experimentally validated.

Retrocopy orthology:
Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
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 ENSMMUG000000195611 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 ENSOPRG00000006029 2 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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