RetrogeneDB ID:

retro_cpor_73

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_158:236313..238200(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000007083
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GSPT1
Ensembl ID:ENSCPOG00000009381
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_73
ATGGATCCGGGCAGCAGCAGCAGCGACTCGGCGCCCGACTACTGGGACCAGGTGGACATGGAAACCCCGAGTTCGGGCCC
GAGCGGGGATGGAATCTCCTCAGAAGTGGCCGAGGCCCAGAGCGAGCATCTCAGCTCGGCCTTCTGCCATCAGCTCAACG
TCAACGCCAAACCCTTCGTGCCTAACGTACACGCCGCGGAGTTCGTGCCGTCCTTCCTGCGGGGCTACGTGCAGCCGCCC
AACCCCCTGGCTGCCTCAGGCGGCACAGATGAAACCTGCACCGGCGCGGGAGATCTTCAAGGTAAACGGTTGGGCCGGGG
GGCACCTGTGGAACCTTGCAAAGATGAAGCGTTAGTATCCTGTGAAGGTTCTTATTCAGCTGTTACCATGGAACTTTCAG
AACCTGTTGTAGAAAATGGAGAGGTGGAAATGGTCCTAGAAGAATCATGGGAGCACAGCAAAGAAGTAAGTGAAGCAGAG
CCTGGGGGCTGTTCCTTGGCAGATTCAGGGCCCCCTGAAGAAAGTGGCCAGGAAATGATGGAGGAGAAAGAGGAATTAAG
AAAATCAAAATCTATGGTCGTACCATCAGGTGCTCCTAAGAAGGAACACGTAAATGTGGTATTCATTGGGCATGTAGATG
CCGGCAAGTCAACCATTGGAGGACAAATAATGTTTTTGACTGGAATGGTTGACAAAAGGACCCTTGAAAAATATGAAAGA
GAAGCCAAGGAAAAAAACAGAGAAACTTGGTATTTGTCCTGGGCTTTAGATACAAATCAGGAAGAACGGGACAAGGGTAA
AACAGTAGAAGTGGGTCGTGCCTATTTCGAAACAGAAAAGAAACATTTCACAATTTTAGATGCTCCTGGCCACAAGAGTT
TTGTCCCGAATATGATTGGGGGTGCTTCTCAAGCTGATTTGGCTGTGCTAGTAATCTCTGCCAGGAAAGGAGAGTTTGAG
ACTGGTTTTGAAAAAGGTGGACAGACAAGGGAGCATGCGATGTTGGCCAAAACAGCAGGGGTAAAACATTTAATAGTGCT
TATCAATAAGATGGATGATCCCACAGTAAATTGGAGCAGCGAGAGATATGAAGAATGTAAAGAAAAGCTAGTGCCCTTTT
TGAAAAAAGTCGGCTTCAGTCCAAAAAAGGATATTCACTTTATGCCCTGCTCAGGACTGACTGGAGCAAATATTAAAGAG
CAGTCAGATTTCTGCCCTTGGTATACTGGGTTACCATTTATTCCATACTTGGATAATTTGCCAAACTTCAACAGATCAGT
TGATGGACCAATTAGGCTGCCAGTTGTGGATAAGTACAAAGATATGGGCACTGTTGTCTTGGGAAAGCTGGAATCAGGAT
CTATTTTTAAAGGCCAGCAGCTTGTGATGATGCCAAACAAGCACAATGTGGAAGTTATTGGAATACTTTCTGATGATACT
GAAACTGATTTTGTAGCTCCAGGTGAAAACCTCAAAATTAGACTGAAGGGAATTGAAGAAGAAGAGATTCTTCCAGGCTT
CATACTTTGTGACCCTAGTAATCTTTGCCATTTTGGACGCACATTTGATGTTCAGATAGTGATTATTGAGCACAAATCTA
TCATCTGCCCAGGTTATAATGCGGTGCTGCACATTCATACTTGTATTGAGGAAGTTGAGATAACAGCCTTAATCTCCTTG
GTAGACAAAAAATCAGGAGAAAAAAGTAAGACACGGCCCCGTTTTGTGAAACAAGACCAAGTGTGCATTGCTCGTTTAAG
GACAGCAGGAACTATCTGCCTGGAGACATTTAAAGATTTTCCTCAGATGGGTCGTTTTACTTTAAGAGATGAGGGTAAGA
CCATTGCAATTGGAAAAGTTCTGAAATTGGTACCAGAGAAAGACTAA

ORF - retro_cpor_73 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.48 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVESSEEQELL-CEGSNSAVSMELSEPVVENGETEMSPEESWEHKEEISEAEPGGGSMGDGRPPEDSAQEM
VE......L..CEGS.SAV.MELSEPVVENGE.EM..EESWEH..E.SEAEPGG.S..D..PPE.S.QEM
RetrocopyVEPCKDEALVSCEGSYSAVTMELSEPVVENGEVEMVLEESWEHSKEVSEAEPGGCSLADSGPPEESGQEM
ParentalMEEEEEMPKPKAVAAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLYSFKRSCEIEMKEV
MEE.EE..K.K....P.GAPKKEHVNVVFIGHVDAGKSTIGGQIM.LTGMVDKRTL....R.......E.
RetrocopyMEEKEELRKSKSMVVPSGAPKKEHVNVVFIGHVDAGKSTIGGQIMFLTGMVDKRTLEKYEREAKEKNRET
ParentalMYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGEF
.YLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGEF
RetrocopyWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGEF
ParentalETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPKKDIHFMP
ETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWS.ERYEECKEKLVPFLKKVGF.PKKDIHFMP
RetrocopyETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSSERYEECKEKLVPFLKKVGFSPKKDIHFMP
ParentalCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPVRLPIVDKYKDMGTVVLGKLESGSICKGQ
CSGLTGAN.KEQSDFCPWY.GLPFIPYLDNLPNFNRSVDGP.RLP.VDKYKDMGTVVLGKLESGSI.KGQ
RetrocopyCSGLTGANIKEQSDFCPWYTGLPFIPYLDNLPNFNRSVDGPIRLPVVDKYKDMGTVVLGKLESGSIFKGQ
ParentalQLVMMPNKHNVEVLGILSDDVETDSVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIVII
QLVMMPNKHNVEV.GILSDD.ETD.VAPGENLKIRLKGIEEEEILPGFILCDP.NLCH.GRTFD.QIVII
RetrocopyQLVMMPNKHNVEVIGILSDDTETDFVAPGENLKIRLKGIEEEEILPGFILCDPSNLCHFGRTFDVQIVII
ParentalEYKSIICPGYNAVLHIHTCIEEVEIKTFICLVDKKSGEKSKTRPRFVKQDQVCIARLKTAGTICLETFKD
E.KSIICPGYNAVLHIHTCIEEVEI...I.LVDKKSGEKSKTRPRFVKQDQVCIARL.TAGTICLETFKD
RetrocopyEHKSIICPGYNAVLHIHTCIEEVEITALISLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETFKD
ParentalFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
FPQMGRFTLRDEGKTIAIGKVLKLVPEKD
RetrocopyFPQMGRFTLRDEGKTIAIGKVLKLVPEKD

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 10 .53 RPM 42 .56 RPM
SRP017611_kidney 1 .57 RPM 72 .65 RPM
SRP017611_liver 0 .26 RPM 56 .41 RPM
SRP040447_lung 1 .26 RPM 40 .53 RPM
SRP040447_skeletal_muscle 0 .16 RPM 34 .04 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_73 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_73 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 25 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095891 retrocopy
retro_amel_4,
Bos taurus ENSBTAG000000035772 retrocopies
retro_btau_1793, retro_btau_1840,
Canis familiaris ENSCAFG000000188561 retrocopy
retro_cfam_2072,
Callithrix jacchus ENSCJAG000000181911 retrocopy
retro_cjac_618,
Cavia porcellus ENSCPOG00000009381 1 retrocopy
retro_cpor_73 ,
Equus caballus ENSECAG000000211951 retrocopy
retro_ecab_739,
Echinops telfairi ENSETEG000000182491 retrocopy
retro_etel_1626,
Felis catus ENSFCAG000000222811 retrocopy
retro_fcat_1913,
Gorilla gorilla ENSGGOG000000040711 retrocopy
retro_ggor_2906,
Microcebus murinus ENSMICG000000141371 retrocopy
retro_mmur_28,
Myotis lucifugus ENSMLUG000000007921 retrocopy
retro_mluc_98,
Macaca mulatta ENSMMUG000000231781 retrocopy
retro_mmul_118,
Monodelphis domestica ENSMODG000000047281 retrocopy
retro_mdom_1420,
Mustela putorius furoENSMPUG000000145041 retrocopy
retro_mputfur_147,
Mus musculus ENSMUSG000000622031 retrocopy
retro_mmus_238,
Nomascus leucogenys ENSNLEG000000101991 retrocopy
retro_nleu_2705,
Oryctolagus cuniculus ENSOCUG000000047591 retrocopy
retro_ocun_1664,
Otolemur garnettii ENSOGAG000000070831 retrocopy
retro_ogar_100,
Pteropus vampyrus ENSPVAG000000050091 retrocopy
retro_pvam_1426,
Rattus norvegicus ENSRNOG000000023351 retrocopy
retro_rnor_2931,
Sarcophilus harrisii ENSSHAG000000059081 retrocopy
retro_shar_14,
Ictidomys tridecemlineatus ENSSTOG000000154061 retrocopy
retro_itri_109,
Tupaia belangeri ENSTBEG000000088732 retrocopies
retro_tbel_3810, retro_tbel_4659,
Tarsius syrichta ENSTSYG000000138122 retrocopies
retro_tsyr_1169, retro_tsyr_148,
Tursiops truncatus ENSTTRG000000116301 retrocopy
retro_ttru_12,


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