RetrogeneDB ID:

retro_psin_1

Retrocopy
location
Organism:Chinese softshell turtle (Pelodiscus sinensis)
Coordinates:JH206250.1:93762..95514(+)
Located in intron of:ENSPSIG00000004298
Retrocopy
information
Ensembl ID:ENSPSIG00000006212
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSPSIG00000017246
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_psin_1
ATGAGGATCCGCCTGGCCAGAAGATGGACTTGGCTTAGCAGAAGCTGCCTGTTGCTTGGGCTCTTGATGGCTGCCTACTT
CCTAGTGGAGCTGTCTGTTTCTACCTTCAGTGCCTCCTCCAGCGGAGACGGCATCACCAATGGGAGATGGGAGAGGCACT
TTTCTGACAGACCAGAAAGAGCAGAGGATCTGGCTCGTCCAGTTTATGAGAAAGCCCCTCCTGATTCTTATGCACTAGGA
GAATGGGGTAAGGCGGCTCGACTACAGTTGACTCCTGAGGAAAAGAAACTGGAAGAAGAACTGATTGAAAAATATGCAAT
TAATATTTATTTGAGTGACAAAATATCTCTACATCGGCATATACAGGACAATCGTATGTATGAATGTAAAGCCAAATCTT
ATAACCATAGAAAACTTCCAACTACATCTGTTATAATTGCTTTCTATAATGAAGCTTGGTCAACTTTATTGAGGACAATC
CACAGCGTTCTTGAAACATCTCCTGCAGTACTTCTAAAAGAAATTATATTAGTAGATGACTTGAGTGATAAAATATATCT
GAAGGCTGAACTTGAAAAGTACATTAGTAACCTGAAAAGAGTTCGTCTGATAAGAACCAGCAAACGAGAAGGACTCGTTC
GTGCACGCTTAATTGGAGCTACTTTTGCTACTGGTGATGTTCTCACATTTCTAGACTGTCATTGTGAGTGTAACTCTGGT
TGGCTGGAACCACTTTTAGAGAGGATCGCTGAGAATGAGACTGTGATAATTTGTCCTGTTATTGATACCATTGATTGGAA
TACATTTGAATTCTATATGCAGACAGGGGAGCCCATGATTGGGGGATTTGATTGGCGATTGACATTTCAGTGGCATTCTG
TGCCTGAACATGAACGTCAAAGATGGAAATCCAAAACTGACCCAATAAGATCCCCAACTATGGCTGGAGGTCTGTTTGCA
GTTAGTAAGAAGTATTTTGAGTATCTTGGTACATATGACACAGGGATGGATGTCTGGGGTGGGGAGAACTTAGAACTGTC
CTTTAGGGTGTGGCAGTGTGGTGGCACGTTAGAGATCCATCCTTGTTCCCATGTAGGCCATGTGTTTCCAAAGCGGGCTC
CATATGCGAGGCCAAATTTCCTTCAGAACACTGCACGTGCTGCTGAAGTGTGGATGGATGAGTATAAAGAACATTTTTAC
AACAGAAATCCTCCAGCAAGAAAAGAAAATTATGGTGATATTTCTGAAAGAAAACTGCTGAGAGAGCGTTTGAAATGTAA
GAATTTTGACTGGTATTTGAAAAATATATTTTCCAACTTACATGTACCAGAGGATCGTCCAGGCTGGCATGGAGCAATCC
ACAGTATGGGAATATCATCAGAATGCCTGGACTACAATTCACCTGAACATAATCCTACTGGAACTCATGTGTCTCTCTTT
GGATGTCATGGTCAAGGAGGCAATCAGTTCTTTGAATACACATCAAGTAAAGAAATTAGGTTTAACTCTGTGACTGAACT
ATGTGCTGAAGTCCCTGAACAAAAGGATTTCATTGGCATGAGGAATTGCCCAAAAGATAGATCCCCTATTCCAGAAAGTA
TCATCTGGCATTTTAAACAGGATGGGACTATTTATCATCCTCAGTCAGGAAAGTGCATTAGTACTTATCGTACTCCTGAG
GGACGGCCTGATGTACAAATGAGGACTTGTAATGCTGCAGATAAAAATCAAATTTGGAAGTTTGAGAAATAA

ORF - retro_psin_1 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.56 %
Parental protein coverage: 99.45 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAASGGAGGARGAPQPPLPAEPER---LRRPVYEKPPLEPGALGELGQAVRLQLSQAEKSLQEASIQQHQI
A.S.G.G...G.........PER...L.RPVYEK.P....ALGE.G.A.RLQL...EK.L.E..I....I
RetrocopyASSSGDGITNGRWERHFSDRPERAEDLARPVYEKAPPDSYALGEWGKAARLQLTPEEKKLEEELIEKYAI
ParentalNIYLSDRISLHRRLPERWHPLCKEKKYDYNNLPKTSVVIAFYNEAWSTLLRTVHSVLETSPDILLEEVIL
NIYLSD.ISLHR.........CK.K.Y....LP.TSV.IAFYNEAWSTLLRT.HSVLETSP..LL.E.IL
RetrocopyNIYLSDKISLHRHIQDNRMYECKAKSYNHRKLPTTSVIIAFYNEAWSTLLRTIHSVLETSPAVLLKEIIL
ParentalVDDYSDKEHLKKPLESYVAGLRKVRLIRANKREGLVRARLLGASLAKGDVLTFLDCHCECHEGWLEPLLE
VDD.SDK..LK..LE.Y...L..VRLIR..KREGLVRARL.GA..A.GDVLTFLDCHCEC..GWLEPLLE
RetrocopyVDDLSDKIYLKAELEKYISNLKRVRLIRTSKREGLVRARLIGATFATGDVLTFLDCHCECNSGWLEPLLE
ParentalRIGEEESAVVCPVIDVIEWNTFEYLGNSGEPQIGGFDWRLVFTWHVIPEKEQKRRRSRTDVIRSPTMAGG
RI.E.E....CPVID.I.WNTFE.....GEP.IGGFDWRL.F.WH..PE.E..R..S.TD.IRSPTMAGG
RetrocopyRIAENETVIICPVIDTIDWNTFEFYMQTGEPMIGGFDWRLTFQWHSVPEHERQRWKSKTDPIRSPTMAGG
ParentalLFAVSKKYFDYLGSYDTGMEVWGGENLEFSFRIWQCGGSLEIHPCSHVGHVFPKQAPYSRAKALANSVRA
LFAVSKKYF.YLG.YDTGM.VWGGENLE.SFR.WQCGG.LEIHPCSHVGHVFPK.APY.R...L.N..RA
RetrocopyLFAVSKKYFEYLGTYDTGMDVWGGENLELSFRVWQCGGTLEIHPCSHVGHVFPKRAPYARPNFLQNTARA
ParentalAEVWMDEYKELYYHRNPHARLEPYGDVTERRLLREKLKCKDFKWFLENIYPELHVPEDRAGFYGMLKNRG
AEVWMDEYKE..Y.RNP.AR.E.YGD..ER.LLRE.LKCK.F.W.L.NI...LHVPEDR.G..G.....G
RetrocopyAEVWMDEYKEHFYNRNPPARKENYGDISERKLLRERLKCKNFDWYLKNIFSNLHVPEDRPGWHGAIHSMG
ParentalMENHCFDYNPPNEHEVTGHRIILYPCHGMGQNQFFEYTSHNEIRYNTRQPEACAAVDSGTDYLTMYLCQD
....C.DYN.P.EH..TG....L..CHG.G.NQFFEYTS..EIR.N....E.CA.V....D...M..C..
RetrocopyISSECLDYNSP-EHNPTGTHVSLFGCHGQGGNQFFEYTSSKEIRFNS-VTELCAEVPEQKDFIGMRNCPK
ParentalNIQNIPENQKFVFREDGTLFHVQTQKCLQAESNSYNGNPAPLLRPCSNSE-YQKWFFKE
....IPE.....F..DGT..H.Q..KC.........G.P....R.C......Q.W.F..
RetrocopyDRSPIPESIIWHFKQDGTIYHPQSGKCI-STYRTPEGRPDVQMRTCNAADKNQIWKFEK

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






RNA-Seq - click to see more details

Pelodiscus sinensis was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pelodiscus sinensis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_psin_1 retrocopy.

TSS - click to see more details

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_psin_1 was not experimentally validated.

Retrocopy orthology:
Pelodiscus sinensis 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 ENSPCAG000000050681 retrocopy
retro_pcap_63,
Pongo abelii ENSPPYG000000194371 retrocopy
retro_pabe_949,
Pelodiscus sinensis ENSPSIG00000017246 1 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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