RetrogeneDB ID:

retro_cpor_1467

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_9:11408338..11409889(+)
Located in intron of:ENSCPOG00000015525
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSCPOG00000012418
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1467
CCGCTCTACGAGAAGCCCCCAGCCGATACCCACGCGCTGGGCGAGTGGGGGCGAGCGAGCAAACTCCAGCTCGGCGAGGG
GGAGCTGAAGCAGCAAGAGGAACTCATCGAGAGGTATGCCATCAACATCTACCTCAGTGACAGGATTTCCCTGCACCGCC
ACATAGAGGACAAAAGAATGTATGAGTGTAAATTCAAGAAGTACGACTACAGGAGGCTTCCCACCACCTCCGTCATCATC
GCCTTCTACAACGAAGCCTGGTCCACCTTGCTGCGCACCATTCACAGCGTTCTGGAGACTTCCCCCGCCGTCCTGTTGAA
GGAGATCATCTTGGTGGATGATTTGAGCGACAGAGTGTATCTGAAGACACAACTGGAAACTTACATCAGCAATCTGGATC
GAGTCCGCTTGATCAGAACCAATAAGCGAGAGGGCCTGGTCCGGGCCCGCCTAATCGGAGCCACTTTTGCCACTGGCGAT
GTCCTCACCTTCCTGGATTGTCACTGTGAGTGTAACTCCGGCTGGCTGGAACCACTCCTGGAAAGGATTGGCGGGGATGA
GACAACAGTCGTTTGTCCTGTGATAGACACCATTGATTGGAATACTTTTGAGTTCTACATGCAGACAGGGGAGCCTATGA
TTGGGGGGTTTGACTGGCGGTTAACGTTCCAGTGGCATTCTGTTCCCAAACATGAAAGGGAGAGGCGGACCTCAAGGATT
GACCCCATCAGGTCGCCCACTATGGCCGGAGGGCTGTTCGCCGTCAGCAAGAAATACTTTGAGTACCTGGGGACCTACGA
CACGGGCATGGAAGTGTGGGGAGGTGAAAACCTCGAGCTGTCTTTTAGGGTGTGGCAGTGCGGTGGCAAATTGGAGATCC
ACCCGTGTTCTCACGTGGGCCATGTGTTCCCTAAGCGGGCGCCCTATGCTCGCCCCAATTTCCTACAGAATACTGCTCGG
GCAGCAGAGGTGTGGATGGATGAATACAAAGAGCATTTCTACAATCGAAACCCTCCAGCACGGAAAGAAGCTTACGGTGA
TATTTCTGAAAGAAAATTATTACGAGAACGGCTAAAATGCAAAAGCTTCGACTGGTATTTGAAAAATGTGTTTTCTAATT
TACACGTCCCAGAGGATAGACCAGGCTGGCACGGGGCTATTCGCAGTTTGGGGATCTCTTCTGAATGTTTAGATTATAAT
TCACCTGACAGCAACCCCACAGGGGCTAACCTTTCACTGTTTGGATGCCACGGTCAAGGAGGCAATCAGTTCTTTGAATA
CACTTCAAACAAAGAAATACGGTTTAATTCCGTGACTGAGCTGTGTGCGGAGGTTCCTGAGCAAAAAAATTACGTAGGGA
TGCAGAACTGTCCTAAAGATGGGTCTCCTGCCCCAGTAAACATCATTTGGCATTTTAAAGATGATGGGACCATCTTCCAT
CCACATTCAGGACTTTGCCTTAGTGCTTATCGGACACCTGAGGGCCGACCTGACGTGCAGATGAGAACTTGTGATGCCCT
AGATAAAAATCAGATCTGGAGGTTTGAGAAA

ORF - retro_cpor_1467 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.15 %
Parental protein coverage: 89.12 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPVLPRPPVPPDALGAQGEAVRLQLQGEELRLQEESVRLHQINIYLSDRISLHRRLPERWNPLCKEKKYDY
P....PP....ALG..G.A..LQL...EL..QEE......INIYLSDRISLHR.........CK.KKYDY
RetrocopyPLYEKPPADTHALGEWGRASKLQLGEGELKQQEELIERYAINIYLSDRISLHRHIEDKRMYECKFKKYDY
ParentalENLPTTSVIIAFYNEAWSTLLRTVYSVLETSPDILVEEVILVDDYSDKEHLKERLANELSGLPKVRLIRA
..LPTTSVIIAFYNEAWSTLLRT..SVLETSP..L..E.ILVDD.SD...LK..L....S.L..VRLIR.
RetrocopyRRLPTTSVIIAFYNEAWSTLLRTIHSVLETSPAVLLKEIILVDDLSDRVYLKTQLETYISNLDRVRLIRT
ParentalSKREGLVRARLLGASVARGNVLTFLDCHCECHEGWLEPLLQRIHEEESAVVCPVIDVIDWNTFEYLGNAG
.KREGLVRARL.GA..A.G.VLTFLDCHCEC..GWLEPLL.RI...E..VVCPVID.IDWNTFE.....G
RetrocopyNKREGLVRARLIGATFATGDVLTFLDCHCECNSGWLEPLLERIGGDETTVVCPVIDTIDWNTFEFYMQTG
ParentalEPQIGGFDWRLVFTWHVVPERDRLRMKSPIDVIRSPTMAGGLFAVSKKYFEYLGSYDTGMEVWGGENLEF
EP.IGGFDWRL.F.WH.VP...R.R..S.ID.IRSPTMAGGLFAVSKKYFEYLG.YDTGMEVWGGENLE.
RetrocopyEPMIGGFDWRLTFQWHSVPKHERERRTSRIDPIRSPTMAGGLFAVSKKYFEYLGTYDTGMEVWGGENLEL
ParentalSFRIWQCGGTLEIHPCSHVGHVFPKQAPYSRSKALANSVRAAEVWMDEFKELYYHRNPRARLEPYGDVTE
SFR.WQCGG.LEIHPCSHVGHVFPK.APY.R...L.N..RAAEVWMDE.KE..Y.RNP.AR.E.YGD..E
RetrocopySFRVWQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDEYKEHFYNRNPPARKEAYGDISE
ParentalRRELRAKLRCRDFRWFLENVYPELHVPEDRPGFFGMLQNKGMKEYCFDYNPPDENQVWGHQVILYNCHGM
R..LR..L.C..F.W.L.NV...LHVPEDRPG..G.....G....C.DYN.PD.N...G....L..CHG.
RetrocopyRKLLRERLKCKSFDWYLKNVFSNLHVPEDRPGWHGAIRSLGISSECLDYNSPDSNPT-GANLSLFGCHGQ
ParentalGQNQFFEYTSQKEIRYNTRQPEACIAVEAGSDTLIMHLC---GDTTPEDQKFLLQEDGSLFHEQSKKCVQ
G.NQFFEYTS.KEIR.N....E.C..V........M..C...G...P.........DG..FH..S..C..
RetrocopyGGNQFFEYTSNKEIRFNS-VTELCAEVPEQKNYVGMQNCPKDGSPAPVNIIWHFKDDGTIFHPHSGLCLS
ParentalAVKKPASQGFVPLLRDCADSDHQKWFFKE
A...P.....V......A....Q.W.F..
RetrocopyAYRTPEGRPDVQMRTCDALDKNQIWRFEK

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
SRP017611_brain 1 .38 RPM 3 .34 RPM
SRP017611_kidney 4 .50 RPM 10 .68 RPM
SRP017611_liver 3 .53 RPM 0 .96 RPM
SRP040447_lung 12 .51 RPM 45 .32 RPM
SRP040447_skeletal_muscle 2 .06 RPM 0 .55 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_1467 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_1467 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus 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 ENSCPOG00000012418 1 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 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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