RetrogeneDB ID:

retro_sscr_32

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:GL892772.2:65646..67395(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000025548
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSSSCG00000005379
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_sscr_32
ATGAGGATCCGGATGGCCGTGAGATGGACGTGGGCAGGCAAAAGCTGCCTGCTGCTGGCGCTCTTAACGGTGGCCTATCT
CCTGGTGGAACTCTCCGTCTCCACTTTGCAAGCCTCGGCGGGAGCCGGTCTCGCCAGGGAGAGGGGGTCAAGACAGCTCT
CAGACTCTGGGAAAAAAGCAGTGGATTTGTCTCGCCCGCTGTATGAGAAGCCGCCTGCAGATTCTCATGCACTTGGGGAG
TGGGGGAAAGGCAGCAAACTGCAGCTCAACGAGGGTGAGCTGAAGCAGCAGGAAGAACTCATTGAGAGATATGCCATTAA
TATTTACCTCAGTGATCGGATTTCCTTGCATCGCCACATAGAGGATAAAAGAATGTACGAATGCAAATCCAAGAAGTTTG
ACTACAGGAGACTTCCCACCACGTCTGTTGTCATCGCTTTCTATAATGAAGCCTGGTCGACTTTGCTCCGCACCATCCAC
AGTGTGTTAGAAACGTCTCCCGCCGTCCTTTTGAAGGAGATCATCTTAGTCGATGACTTGAGTGACAGGGTTTATTTGAA
GACACAACTTGAAACTTACATCAGCAATCTCGATAGAGTCCGCTTGATTAGAACAAATAAGCGGGAGGGGCTGGTTAGGG
CTCGTCTGATTGGGGCCACTTTTGCCACTGGGGATGTCCTTACTTTCCTGGATTGTCACTGTGAGTGTAATACGGGTTGG
TTGGAGCCGCTTTTGGAAAGGATTGCTGAAGATGAAACAGCCATCGTTTGTCCTGTTATAGACACCATTGACTGGAATAC
TTTTGAGTTCTATATGCAGACTGGGGAGCCTATGATTGGTGGCTTTGACTGGCGTTTAACATTCCAGTGGCATTCTGTCC
CCAAACACGAAAGGGACCGGCGGAAATCGAGAATTGACCCTATCCGATCGCCCACCATGGCTGGAGGACTGTTTGCCGTC
AGCAAGAAATACTTTCAGTACCTGGGAACGTATGACACTGGGATGGAAGTGTGGGGAGGTGAGAACCTCGAGCTGTCTTT
CAGGGTGTGGCAGTGTGGAGGTAAACTGGAGATCCACCCGTGTTCCCACGTGGGCCACGTATTCCCCAAGCGGGCACCGT
ATGCTCGGCCCAACTTCCTGCAGAATACTGCTCGGGCAGCGGAAGTGTGGATGGACGAGTACAAAGAGCATTTCTACAAT
CGAAACCCTCCAGCCCGGAAGGAAGCCTACGGAGATATTTCCGAAAGAAAATTACTCCGGGAGCGGCTGGGATGCAAGAG
CTTTGACTGGTATTTGAAAAACGTGTTTTCGAATTTACATGTTCCAGAGGACAGGCCAGGCTGGCATGGGGCTATTCGCA
GTATAGGTATCTCTTCTGAATGTTTAGATTATAATTCTCCTGAAAACAACCCCACAGGTGCTAACCTTTCACTCTTTGGC
TGCCACGGCCAAGGAGGCAACCAATTCTTTGAATATACTTCAAACCGAGAAATAAGGTTTAATTCCGTGACAGAGTTATG
TGCAGAGGTGCCTGAACAAAAAAATCACGTGGGGATGCAGAATTGTCCCAAAGACGGGTCTCCTATTCCAACCAACATTA
TTTGGCATTTTAAAGAAGATGGAACCATTTTTCATCCCCACTCGGGGCTGTGTCTCAGTGCTTACCGGACACCTGAGGGC
CGACCTGATGTTCAGATGAGAACGTGTGATGCTGCAGATAAAAATCAAATCTGGAAGTTTGAGAAGTAG

ORF - retro_sscr_32 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.09 %
Parental protein coverage: 67.12 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPVLPRPPVSEDSLGAHGEAVWLQLQGEELRLQEESLRLHQINIYLSDRISLHRRLPERWNPLCKEKKYDY
P....PP.....LG..G....LQL...EL..QEE......INIYLSDRISLHR.........CK.KK.DY
RetrocopyPLYEKPPADSHALGEWGKGSKLQLNEGELKQQEELIERYAINIYLSDRISLHRHIEDKRMYECKSKKFDY
ParentalDHLPTTSVVIAFYNEAWSTLLRTVYSVLETSPDILLEEVILVDDYSDREHLKERLAIELAKLPKVRLIRA
..LPTTSVVIAFYNEAWSTLLRT..SVLETSP..LL.E.ILVDD.SDR..LK..L......L..VRLIR.
RetrocopyRRLPTTSVVIAFYNEAWSTLLRTIHSVLETSPAVLLKEIILVDDLSDRVYLKTQLETYISNLDRVRLIRT
ParentalNKREGLVRARLLGASVAKGDVLTFLDCHCECHEGWLEPLLQRIHEKESAVVCPVIDVIDWNTFEYMGNSR
NKREGLVRARL.GA..A.GDVLTFLDCHCEC..GWLEPLL.RI.E.E.A.VCPVID.IDWNTFE......
RetrocopyNKREGLVRARLIGATFATGDVLTFLDCHCECNTGWLEPLLERIAEDETAIVCPVIDTIDWNTFEFYMQTG
ParentalEPQIGGFDWRLVFTWHVVPERERLRMKSPIDVIRSPTMAGGLFAVSKKYFEYLGAYDTGMEVWGGENLEF
EP.IGGFDWRL.F.WH.VP..ER.R.KS.ID.IRSPTMAGGLFAVSKKYF.YLG.YDTGMEVWGGENLE.
RetrocopyEPMIGGFDWRLTFQWHSVPKHERDRRKSRIDPIRSPTMAGGLFAVSKKYFQYLGTYDTGMEVWGGENLEL
ParentalSFRIWQCGGTLEIHPCSHVGHVFPKQAPYSRSKALANSVRAAEVWMDEFKELYYHRNPHARLEPFGDVTE
SFR.WQCGG.LEIHPCSHVGHVFPK.APY.R...L.N..RAAEVWMDE.KE..Y.RNP.AR.E..GD..E
RetrocopySFRVWQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDEYKEHFYNRNPPARKEAYGDISE
ParentalRKQLRAKLQCKDFKWFLETVYPELHVPEDRPGFFGMVLSRGL
RK.LR..L.CK.F.W.L..V...LHVPEDRPG..G...S.G.
RetrocopyRKLLRERLGCKSFDWYLKNVFSNLHVPEDRPGWHGAIRSIGI

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
SRP014902_placenta 0 .00 RPM 32 .78 RPM
SRP014902_testis 0 .00 RPM 17 .82 RPM
SRP018288_heart 0 .00 RPM 0 .60 RPM
SRP018288_kidney 0 .00 RPM 6 .50 RPM
SRP018288_liver 0 .00 RPM 0 .16 RPM
SRP018288_lung 0 .00 RPM 3 .46 RPM
SRP018856_adipose 0 .00 RPM 4 .76 RPM
SRP035408_brain 0 .00 RPM 0 .22 RPM
SRP035408_liver 0 .00 RPM 0 .09 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_32 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_32 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_32 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Canis familiaris retro_cfam_683
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 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 ENSSSCG00000005379 1 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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