RetrogeneDB ID:

retro_pabe_949

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:12:90396839..90398240(-)
Located in intron of:ENSPPYG00000004819
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSPPYG00000019437
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_pabe_949
CTGCATCGACACATAGAGGATAAAAGAATGTATGAGTGTAAGTCCCAGAAGTTCAACTATAGGACACTTCCTACCACCTC
TGTTATCATTGCTTTCTATAACGAAGCCTGGTCGACTTTGCTCCGTACCATTCACAGTGTTTTAGAAACTTCTCCTGCAG
TTCTTTTGAAAGAGATCATCTTGGTGGATGACTTGAGTGACAGAGTTTATTTGAAGACACAACTTGAAACTTACATCAGC
AATCTTGATAGAGTACGCTTGATTAGGACCAATAAGCGAGAGGGGCTGGTTAGGGCCCGTCTGATTGGGGCCACTTTCGC
CACTGGGGACGTCCTCACTTTCCTGGATTGTCACTGTGAGTGTAATTCCGGTTGGCTGGAACCGCTTTTGGAAAGGATTG
GGAGAGATGAAACAGCAATTGTGTGTCCTGTTATAGACACAATTGATTGGAATACTTTTGAATTCTATATGCAGACAGGG
GAGCCCATGATTGGTGGGTTTGACTGGCGTTTAACATTTCAGTGGCATTCTGTCCCCAAACAGAAAAGGGACAGGCAGAT
ATCAAGAATTGACCCCATCAGATCACCTACCATGGCTGGAGGACTGTTTGCTGTCAGCAAGAAATATTTTCAGTACCTTG
GAACGTATGACACAGGAATGGAAGTGTGGGGAGGTGAAAACCTTGAGCTGTCTTTTAGGGTGTGGCAGTGTGGTGGCAAA
TTGGAGATCCACCCGTGTTCCCACGTGGGCCATGTGTTCCCCAAGCGGGCACCATATGCTCGCCCCAATTTCCTACAGAA
TACTGCTCGGGCAGCAGAAGTTTGGATGGATGAGTACAAAGAGCACTTCTACAATAGAAACCCTCCAGCAAGAAAAGAAG
CTTATGGTGATATTTCTGAAAGAAAATTACTACGAGAGCGGCTGAGATGCAAGAGCTTTGACTGGTATTTGAAAAACGTT
TTTCCTAATTTACATGTTCCAGAGGATAGACCAGGCTGGCATGGGGCTATTCGCAGTAGAGGGATCTCGTCTGAATGTTT
AGATTATAATTCTCCTGACAACAACCCCACAGGTGCTAACCTTTCACTGTTTGGATGCCATGGTCAAGGAGGCAATCAAT
TCTTTGAATATACTTCAAACAAAGAAATAAGGTTTAATTCTGTGACAGAGTTATGTGCAGAGGTACCTGAGCAAAAAAAT
TATGTAGGAATGCAAAATTGTCCCAAAGATGGGTTCCCTGTACCAGCAAACATTATTTGGCATTTTAAAGAAGATGGAAC
TATTTTTCACCCACACTCAGGACTGTGTCTTAGTGCTTATCGGACACCGGAGGGCCGACCTGATGTACAAATGAGAACTT
GTGATGCTCTAGATAAAAATCAAATTTGGAGTTTTGAGAAA

ORF - retro_pabe_949 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.28 %
Parental protein coverage: 99.36 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMHRRLPERWNPLCKEKKYDYDNLPRTSVIIAFYNEAWSTLLRTVYSVLETSPDILLEEVILVDDYSDREH
.HR.........CK..K..Y..LP.TSVIIAFYNEAWSTLLRT..SVLETSP..LL.E.ILVDD.SDR..
RetrocopyLHRHIEDKRMYECKSQKFNYRTLPTTSVIIAFYNEAWSTLLRTIHSVLETSPAVLLKEIILVDDLSDRVY
ParentalLKERLANELSGLPKVRLIRANKREGLVRARLLGASAARGDVLTFLDCHCECHEGWLEPLLQRIHEEESAV
LK..L....S.L..VRLIR.NKREGLVRARL.GA..A.GDVLTFLDCHCEC..GWLEPLL.RI...E.A.
RetrocopyLKTQLETYISNLDRVRLIRTNKREGLVRARLIGATFATGDVLTFLDCHCECNSGWLEPLLERIGRDETAI
ParentalVCPVIDVIDWNTFEYLGNSGEPQIGGFDWRLVFTWHTVPERERIRMRSPVDVIRSPTMAGGLFAVSKKYF
VCPVID.IDWNTFE.....GEP.IGGFDWRL.F.WH.VP...R.R..S..D.IRSPTMAGGLFAVSKKYF
RetrocopyVCPVIDTIDWNTFEFYMQTGEPMIGGFDWRLTFQWHSVPKQKRDRQISRIDPIRSPTMAGGLFAVSKKYF
ParentalEYLGSYDTGMEVWGGENLEFSFRIWQCGGVLETHPCSHVGHVFPKQAPYSRNKALANSVRAAEVWMDEFK
.YLG.YDTGMEVWGGENLE.SFR.WQCGG.LE.HPCSHVGHVFPK.APY.R...L.N..RAAEVWMDE.K
RetrocopyQYLGTYDTGMEVWGGENLELSFRVWQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDEYK
ParentalELYYHRNPRARLEPFGDVTERKQLRAKLQCKDFKWFLETVYPELHVPEDRPGFFGMLQNKGLTDYCFDYN
E..Y.RNP.AR.E..GD..ERK.LR..L.CK.F.W.L..V.P.LHVPEDRPG..G.....G....C.DYN
RetrocopyEHFYNRNPPARKEAYGDISERKLLRERLRCKSFDWYLKNVFPNLHVPEDRPGWHGAIRSRGISSECLDYN
ParentalPPDENQIVGHQVILYLCHGMGQNQFFEYTSQKEIRYNTHQPEGCIAVEAGMDTLIMHLCEE---TAPENQ
.PD.N...G....L..CHG.G.NQFFEYTS.KEIR.N....E.C..V........M..C.......P.N.
RetrocopySPDNNP-TGANLSLFGCHGQGGNQFFEYTSNKEIRFNS-VTELCAEVPEQKNYVGMQNCPKDGFPVPANI
ParentalKFILQEDGSLFHEQSKKCVQAARKESSDSFIPLLRDCTNSNNQKWFFKE
.....EDG..FH..S..C..A.R..................NQ.W.F..
RetrocopyIWHFKEDGTIFHPHSGLCLSAYRTPEGRPDVQMRTCDALDKNQIWSFEK

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 .44 RPM 3 .76 RPM
SRP007412_cerebellum 1 .22 RPM 55 .69 RPM
SRP007412_heart 0 .84 RPM 1 .54 RPM
SRP007412_kidney 3 .48 RPM 13 .69 RPM
SRP007412_liver 2 .42 RPM 1 .90 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_949 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_949 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_949 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_777
Gorilla gorilla retro_ggor_890
Macaca mulatta retro_mmul_888
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 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 ENSOPRG000000060292 retrocopies
retro_opri_121, retro_opri_515,
Procavia capensis ENSPCAG000000050681 retrocopy
retro_pcap_63,
Pongo abelii ENSPPYG00000019437 1 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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