RetrogeneDB ID:

retro_ocun_1664

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:GL018748:1207063..1208629(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000014736
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GSPT1
Ensembl ID:ENSOCUG00000004759
Aliases:None
Description:G1 to S phase transition 1 [Source:HGNC Symbol;Acc:4621]


Retrocopy-Parental alignment summary:






>retro_ocun_1664
GGACGGGGGGCACCTGTGGAACCTCCCAAAGAACTGTTAGTGTGTGAAGGTTCCAATTCAGCCGTTACCATGGAACTTTC
AGAACCTCTTATAGAAAATGGAGAGGTGGAAATGATCTTAGAAGAATCATGGGAGCACAGTAAAGAAGTAAGTGAAGCAG
AGCCTGGGGGTTGTGTCTTGGGCGATTCGGGGCCCCCAGAAGAAAGTGGCCAGGAGATGATGGAGGAGAAAGAGGAGACC
AGAAAATCCAAATCCTCTGTCGTACCCTCAGGTGCTCCCAAAAAAGAACACGTAAATGTGGTGTTCATTGGGCATGTGGA
TGCCGGCAAGTCCACCATTGGAGGGCAGATAATGTTTTTAACTGGAATGGTTGACAAAAGGACACTTGAGAAATACGAAC
GAGAAGCTAAGGAAAAAAACAGAGAAACTTGGTATTTGTCCTGGGCGTTAGATACCAACCAGGAAGAACGAGACAAGGGA
AAAACCGTAGAAGTGGGTCGTGCCTATTTTGAAACTGAAAAGAAACATTTCACGATTTTAGATGCCCCTGGCCATAAGAG
TTTTGTCCCAAATATGATTGGTGGTGCCTCTCAAGCTGATCTGGCTGTGCTGGTCATCTCTGCCAGGAAGGGAGAGTTTG
AGACTGGATTTGAAAAAGGTGGACAGACGAGAGAACATGCGATGTTGGCCAAAACAGCAGGGGTAAAACATTTGGTTGTG
CTTATTAATAAGATGGATGACCCCACGGTGAATTGGAGCTGTGAGAGGTATGAAGAATGTAAAGAAAAACTGGTGCCGTT
TTTGAAAAAAGTCGGCTTCAGTCCCAAAAAGGACATTCACTTCATGCCCTGCTCAGGACTGACTGGGGCTAACATTAAAG
ACCAGTCAGAGCTCTGCCCCTGGTACACTGGATTACCATTCATTCCGTATTTGGATAATTTGCCAAACTTCAACAGGTCG
ATTGATGGGCCAATCAGGCTCCCAATTGTTGACAAGTACAAGGATATGGGTACTGTGGTCCTGGGCAAGCTGGAATCGGG
ATCCATTTATAAAGGCCAACAGCTCGTGATGATGCCAAATAAACACAATGTGGAAGTTCTTGGAATTCTTTCTGACGATA
CTGAGACTGATTTTGTGGCCCCAGGTGAAAACCTCAAAATCAGGCTGAAGGGGATTGAAGAAGAAGAGATTCTTCCCGGA
TTCATCCTTTGTGACCCTAGCAATCTTTGCCATTCCGGACGCACATTCGATGTCCAGATAGTGATTATTGAGCACAAATC
CATCATCTGTCCAGGTTATAATGCGGTGCTGCACATCCACACTTGCATTGAGGAAGTTGAGATAACAGCCTTAATCTCCC
TCGTCGACAAAAAGTCAGGAGAAAAAAGTAAGACACGGCCCCGCTTCGTGAAGCAAGATCAAGTGTGCATTGCCCGATTA
AGGACAGCCGGGACTATCTGCCTTGAGACTTTTAAAGACTTTCCTCAGATGGGCCGCTTCACTTTGAGAGATGAGGGTAA
GACCATTGCAATTGGAAAAGTTCTGAAACTGGTTCCAGAGAAGGAC

ORF - retro_ocun_1664 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.44 %
Parental protein coverage: 81.97 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalGPSAPVESSQEEQSLCEGSVSAVSMELSEPVVENGETEMSPEESWEHKEEISEAEPGGGSLGDGRPPEEG
G..APVE...E....CEGS.SAV.MELSEP..ENGE.EM..EESWEH..E.SEAEPGG..LGD..PPEE.
RetrocopyGRGAPVEPPKE-LLVCEGSNSAVTMELSEPLIENGEVEMILEESWEHSKEVSEAEPGGCVLGDSGPPEES
ParentalAQEMMEEEEEMPKPKSVAAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYEREAKEK
.QEMMEE.EE..K.KS...P.GAPKKEHVNVVFIGHVDAGKSTIGGQIM.LTGMVDKRTLEKYEREAKEK
RetrocopyGQEMMEEKEETRKSKSSVVPSGAPKKEHVNVVFIGHVDAGKSTIGGQIMFLTGMVDKRTLEKYEREAKEK
ParentalNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISAR
NRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISAR
RetrocopyNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISAR
ParentalKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPKKDI
KGEFETGFEKGGQTREHAMLAKTAGVKHL.VLINKMDDPTVNWS.ERYEECKEKLVPFLKKVGF.PKKDI
RetrocopyKGEFETGFEKGGQTREHAMLAKTAGVKHLVVLINKMDDPTVNWSCERYEECKEKLVPFLKKVGFSPKKDI
ParentalHFMPCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPIRLPIVDKYKDMGTVVLGKLESGSI
HFMPCSGLTGAN.K.QS..CPWY.GLPFIPYLDNLPNFNRS.DGPIRLPIVDKYKDMGTVVLGKLESGSI
RetrocopyHFMPCSGLTGANIKDQSELCPWYTGLPFIPYLDNLPNFNRSIDGPIRLPIVDKYKDMGTVVLGKLESGSI
ParentalCKGQQLVMMPNKHNVEVLGILSDDVETDSVAPGENLKIRLKGIEEEEILPGFILCDLNNLCHSGRTFDAQ
.KGQQLVMMPNKHNVEVLGILSDD.ETD.VAPGENLKIRLKGIEEEEILPGFILCD..NLCHSGRTFD.Q
RetrocopyYKGQQLVMMPNKHNVEVLGILSDDTETDFVAPGENLKIRLKGIEEEEILPGFILCDPSNLCHSGRTFDVQ
ParentalIVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLE
IVIIEHKSIICPGYNAVLHIHTCIEEVEITALI.LVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLE
RetrocopyIVIIEHKSIICPGYNAVLHIHTCIEEVEITALISLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLE
ParentalTFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
TFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
RetrocopyTFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD

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 14 .40 RPM 55 .13 RPM
SRP017611_kidney 3 .55 RPM 89 .80 RPM
SRP017611_liver 0 .31 RPM 43 .08 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_1664 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1664 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1664 has 0 orthologous retrocopies within eutheria group .

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 ENSCPOG000000093811 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 ENSOCUG00000004759 1 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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