RetrogeneDB ID:

retro_pcap_63

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:GeneScaffold_3638:148227..149778(-)
Located in intron of:ENSPCAG00000002158
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSPCAG00000005068
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_pcap_63
CCACTGTATGTAAAGCCCCCTGCTGATTCCCATGCCCTGGGGGAGTGGGGGAAAGCCAGCAAACTGCAGCTCAGTGACGG
TGAACGGAAGAAGGTAGAAGAGCTGATTGAGAGATACGCCATCAATATTTACCTCAGTGACAGGATATCCCTGCACCGTC
ACATAGAGGATAAAAGGATGTATGAGTGTAAATCCAAGAAGTTCAACTATAGGAGACTTCCCACTACGTCGGTTGTCATC
GCTTTCTACAACGAAGCTTGGTCGACTTTACTTCGCACCATTCACAGTGTTTTAGAAACTTCTCCCGCAGTCCTTTTGAA
GGAGATCATCTTGGTAGATGACTTGAGTGACCGAGTTTATTTGAAGGCACAGCTGGAAAGTTACATCAGCAATCTCGAAA
GAGTCCGCTTGATAAGAACCAAAAAGCGAGAGGGGCTGGTTAGGGCCCGCCTGATTGGGGCCACTTTTGCCACTGGCGAT
GTCCTCACTTTCCTAGATTGTCACTGTGAATGTACTTCTGGTTGGCTTGAACCACTTTTGGAAAGGATCAGTCAAGATGA
AACAGCAATTGTTTGTCCTGTCATAGACACCATTGATTGGAACACTTTTGAATACTACATGCAGACAGGGGAGCCCATGA
TTGGTGGGTTTGACTGGCGTTTAACATTCCAGTGGCATTCTGTCCCCAAACATGAAAGGGACAGGAGATCTTCAAGAATT
GACCCCATCAGATCGCCCACTATGGCTGGAGGACTGTTTGCTGTCAGCAAGAAATATTTTGAGTACCTTGGAACGTATGA
TACTGGAATGGAAGTGTGGGGAGGTGAAAACCTAGAACTATCTTTTAGAGTGTGGCAGTGCGGTGGTAAGTTGGAGATCG
ACCCGTGTTCCCACGTGGGCCATGTATTCCCAAAGCGGGCACCCTATTCTAGACCCAATTTCCTACAGAATACTGCCCGG
GCAGCAGAAGTATGGATGGATGAATACAAACAGCATTTCTACAATCGAAACCCTCCAGCAAGAAAAGAAGCTTATGGGGA
TATTTCTGAAAGAAAATTACTACGAGAACGGCTGAGATGCAGGAGTTTTGACTGGTATTTAAAAAATGTGTTTTCTAGTT
TACATGTGCCAGAGGATAGGCCAGGCTGGCATGGAGCTATTCACAGTATTGGGATTTCTTCTGAATGCTTAGATTATAAT
TCTCCTGACAATAACCCCACAGGGGCTAACCTCTCACTATTTGGATGCCATGGCCAGGGAGGAAATCAGTTCTTTGAATA
TACTTCAAACAAAGAGATAAGGTTTAATTCTGTGACAGAGTTATGTGCCACAGTCCCTGAGCAAAAGAATTACGTTGGAA
TGCAAACTTGTCCTAGAGATGGATTCTCTATTCCAGCAAACATTATTTGGCATTTTAAGGAAGATGGAACCATTTTTCAT
CCACACTCAGGACTGTGCCTGAGTGCTTATTGGACGGCTGAGGGCCGGGCTGATGTACAGATGAGAACTTGTAATACTGT
AGACAAAAATCAAATCTGGAGGTTTGAGAAA

ORF - retro_pcap_63 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.92 %
Parental protein coverage: 89.58 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalPVLLRPPVPVDALGAKGEAVRLQLQGEELRLQEESVQLHQINIYLSDRISLHRRLPERRNPLCLEKKYDY
P....PP....ALG..G.A..LQL...E....EE......INIYLSDRISLHR.....R...C..KK..Y
RetrocopyPLYVKPPADSHALGEWGKASKLQLSDGERKKVEELIERYAINIYLSDRISLHRHIEDKRMYECKSKKFNY
ParentalENLPSTSVIIAFYNEAWSTLLRTVYSVLETSSDMLLEEVILVDDYSDREHLKERLAVELSRLPKVRLIRA
..LP.TSV.IAFYNEAWSTLLRT..SVLETS...LL.E.ILVDD.SDR..LK..L....S.L..VRLIR.
RetrocopyRRLPTTSVVIAFYNEAWSTLLRTIHSVLETSPAVLLKEIILVDDLSDRVYLKAQLESYISNLERVRLIRT
ParentalHKREGLVRARLLGASVAKGDVLTFLDCHCECHEGWLEPLLERIHEEESAVVCPVIDVIDWDTFEYLGNPG
.KREGLVRARL.GA..A.GDVLTFLDCHCEC..GWLEPLLERI...E.A.VCPVID.IDW.TFEY....G
RetrocopyKKREGLVRARLIGATFATGDVLTFLDCHCECTSGWLEPLLERISQDETAIVCPVIDTIDWNTFEYYMQTG
ParentalEPQIGGFDWRLVFTWHTVPERERKRMRSPIDVIXXXXMAGGLFAVSKKYFDYLGSYDTGMEVWGGENLEF
EP.IGGFDWRL.F.WH.VP..ER.R..S.ID.I....MAGGLFAVSKKYF.YLG.YDTGMEVWGGENLE.
RetrocopyEPMIGGFDWRLTFQWHSVPKHERDRRSSRIDPIRSPTMAGGLFAVSKKYFEYLGTYDTGMEVWGGENLEL
ParentalSFRIWQCGGTLETHPCSHVGHVFPKKAPYSRSKALANSVRAAEVWMDEYKELYYHRNPHARLEPFGDVTE
SFR.WQCGG.LE..PCSHVGHVFPK.APYSR...L.N..RAAEVWMDEYK...Y.RNP.AR.E..GD..E
RetrocopySFRVWQCGGKLEIDPCSHVGHVFPKRAPYSRPNFLQNTARAAEVWMDEYKQHFYNRNPPARKEAYGDISE
ParentalRRELRAKLQCKDFRWFLQTVYPELHVPEDRPGFFGMLQNKGLKGYCFDYNPPTENQVLGHEVLLYKCHGM
R..LR..L.C..F.W.L..V...LHVPEDRPG..G.....G....C.DYN.P..N...G....L..CHG.
RetrocopyRKLLRERLRCRSFDWYLKNVFSSLHVPEDRPGWHGAIHSIGISSECLDYNSP-DNNPTGANLSLFGCHGQ
ParentalGQNQFFEYTSQNEIRYNTRQPECCVSVAADSDVLIMEFCKA---ATPEDQKFILREDGSLFHVQSQKCVQ
G.NQFFEYTS..EIR.N....E.C..V........M..C.......P........EDG..FH..S..C..
RetrocopyGGNQFFEYTSNKEIRFNS-VTELCATVPEQKNYVGMQTCPRDGFSIPANIIWHFKEDGTIFHPHSGLCLS
ParentalADKKTPNGSLMPLLRDCSNMER-QKWFFKE
A...T..G......R.C......Q.W.F..
RetrocopyA-YWTAEGRADVQMRTCNTVDKNQIWRFEK

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






RNA-Seq - click to see more details

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Procavia capensis was not studied using ChIP-Seq data.

EST - click to see more details

Procavia capensis was not studied using EST data.

TSS - click to see more details

Procavia capensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_pcap_63 was not experimentally validated.

Retrocopy orthology:
Procavia capensis 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 ENSOPRG000000060292 retrocopies
retro_opri_121, retro_opri_515,
Procavia capensis ENSPCAG00000005068 1 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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