RetrogeneDB ID:

retro_btau_1840

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:X:94378603..94380436(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000013311
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BT.22451
Ensembl ID:ENSBTAG00000003577
Aliases:None
Description:eukaryotic peptide chain release factor GTP-binding subunit ERF3A [Source:RefSeq peptide;Acc:NP_001091540]


Retrocopy-Parental alignment summary:






>retro_btau_1840
ATGGAAGCACCGGGTTTGGCCCCGAGCGGGGACCGAGCCTCCTCGGCGTTGGCGGCGGTCGCCGCCGAGGTGCAGCATGA
GCCCCTCAGCTCGGCCTTCAGCCGTCAGCTCAACATCAACGCCAAACCCTTCGTGCCTAACGTCCATGCCGCGGAGTTCG
TGCCGGCCTTCCTGCGGGGCCCGAGCCAGCCGCAGACCCCCCCGAATGACGCCCCCGGATTCTATGAAACCTGTACGGGC
GCGGGCGACCCTCAAGGTAAAAGGCTGGGACGGGGGGCACCTGTGGAACATTCCAAAGAGGAACAGTTATTGTGGCGTGA
AGGTTCCAATTCAGCCGTTACCATGGAACTTTCAGAACCTGTTGTAGAAAATGGAGAGGTGGAGATGGTTTTAGAAGAGT
CATGGGAGCACAATGAAGTAAGTGAAGCCGAGCCAGGGGGTAGTTCCTTGGGAGATTCGGGGCCCCCAGAAGAAAGTGGC
CAGGAAATGATGGAGAAAGAGGAAATCAGAAAATCGAAATCTGTGGTCGTACCCTCAGGTGCTCCTAAAAAAGAACACGT
AAATGTGGTATTCATTGGGCATGTTGATGCCGGGAAGTCAACCATTGGAGGACAGATCATGTTTTTGACAGGAATGGTTG
ACAAAAGAACACTTGAGAAATATGAAAGAGAAGCTAAAGAAAAAAACAGAGAAACTTGGTATTTGTCCTGGGCCTTAGAT
ACAAACCAGGAAGAACGAGACAAGGGTAAAACAGTAGAAGTGGGTCGTGCCTATTTTGAAACAGAAAAGAAACATTTCAC
AATTTTAGATGCCCCTGGCCATAAGAGTTTTGTCCCAAATATGATCGGTGGTGCTTCTCAAGCTGATTTGGCTGTACTGG
TAATCTCTGCCAGGAAAGGAGAGTTTGAGACTGGATTTGAAAAAGGTGGACAGACAAGAGAACATGCAATGTTGGCAAAA
ACGGCAGGGGTGAAATATTTGATAGTGCTTATTAATAAGATGGATGATCCCACAGTAAATTGGAGCATTGAAAGATATGA
AGAATGTAAAGAAAAGCTAGTGCCCTTTTTGAAAAAAGTCGGCTTTAGTCCCAAAAAGGACATTCACTTTATGCCCTGCT
CAGGGCTGACCGGGGCAAATATTAAAGAGCAATCAGATTTCTGCCCTTGGTACACTGGATTACCATTCATTCCCTATTTG
GATAATATGCCAAACTTCAACAGATCCATTGATGGACCAATTAGACTGCCAATTGTGGATAAGTACAAGGATATGGGCAC
TGTGGTCCTGGGAAAGCTGGAATCAGGATCCATTTTTAAAGGCCAGCAGCTTGTGATGATGCCAAACAAGCACAATGTGG
AAGTTCTTGGAATACTTTCTGATGATGCTGAAACTGATTATGTAGCCCCAGGTGAAAACCTTAAAATCAGACTGAAGGGA
ATTGAAGAAGAAGAGATTCTTCCAGGATTCATACTCTGTGATCCTACTAATCTTTGCCATTCTGGACGCACATTTGATGT
TCAGATAGTGATTATTGAGCACAAATCCATCATCTGCCCAGGTTATAATGCAGTGCTGCACATTCATACTTGTATTGAGG
AAGTTGAGATAACAGCCTTAATCTCCTTGGTAGATAAAAAATCAGGAGAAAAGAGTAAGACACGGCCCCGCTTCGTGAAG
CAAGATCAAGTGTGCATTGCCCGTTTAAGGACAGCAGGAACTATCTGCCTTGAGACATTCAAAGATTTTCCTCAGATGGG
TCGTTTTACTTTAAGAGATGAGGGTAAGACCATTGCAATTGGCAAAGTTCTGAAACTGGTCCCAGAGAAGGAC

ORF - retro_btau_1840 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.44 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMEAPGPGPCGG-AGGPLAAAAAEAQREHLSAAFSRQLNVNAKPFVPNVHAAEFVPSFLRGPA--QLPASP
MEAPG..P.G..A...LAA.AAE.Q.E.LS.AFSRQLN.NAKPFVPNVHAAEFVP.FLRGP...Q.P...
RetrocopyMEAPGLAPSGDRASSALAAVAAEVQHEPLSSAFSRQLNINAKPFVPNVHAAEFVPAFLRGPSQPQTPPND
ParentalA-GAAANNHGAGNGAG---GPSAPVESSQEEQSLLCEGSNSAVSMELSEPI-ENGETEMSPEESWEHKEE
A.G......GAG...G...G..APVE.S.EEQ.L..EGSNSAV.MELSEP..ENGE.EM..EESWEH.E.
RetrocopyAPGFYETCTGAGDPQGKRLGRGAPVEHSKEEQLLWREGSNSAVTMELSEPVVENGEVEMVLEESWEHNE-
ParentalISEAEPDGGSLGDGRPAEESAQEMMEEEEEIPKPKSVVAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMY
.SEAEP.G.SLGD..P.EES.QEMME.EE.I.K.KSVV.P.GAPKKEHVNVVFIGHVDAGKSTIGGQIM.
RetrocopyVSEAEPGGSSLGDSGPPEESGQEMMEKEE-IRKSKSVVVPSGAPKKEHVNVVFIGHVDAGKSTIGGQIMF
ParentalLTGMVDKRTLEKYEREAKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFV
LTGMVDKRTLEKYEREAKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFV
RetrocopyLTGMVDKRTLEKYEREAKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFV
ParentalPNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEE
PNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVK.LIVLINKMDDPTVNWS.ERYEE
RetrocopyPNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKYLIVLINKMDDPTVNWSIERYEE
ParentalCKEKLVPFLKKVGFNPKKDIHFMPCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPIRLPI
CKEKLVPFLKKVGF.PKKDIHFMPCSGLTGAN.KEQSDFCPWY.GLPFIPYLDN.PNFNRS.DGPIRLPI
RetrocopyCKEKLVPFLKKVGFSPKKDIHFMPCSGLTGANIKEQSDFCPWYTGLPFIPYLDNMPNFNRSIDGPIRLPI
ParentalVDKYKDMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDSVAPGENLKIRLKGIEEEEILP
VDKYKDMGTVVLGKLESGSI.KGQQLVMMPNKHNVEVLGILSDD.ETD.VAPGENLKIRLKGIEEEEILP
RetrocopyVDKYKDMGTVVLGKLESGSIFKGQQLVMMPNKHNVEVLGILSDDAETDYVAPGENLKIRLKGIEEEEILP
ParentalGFILCDPNNLCHSGRTFDAQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRF
GFILCDP.NLCHSGRTFD.QIVIIEHKSIICPGYNAVLHIHTCIEEVEITALI.LVDKKSGEKSKTRPRF
RetrocopyGFILCDPTNLCHSGRTFDVQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALISLVDKKSGEKSKTRPRF
ParentalVKQDQVCIARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
VKQDQVCIARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
RetrocopyVKQDQVCIARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD

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
ERP005899_liver 13 .91 RPM 36 .62 RPM
ERP005899_muscle 3 .43 RPM 74 .27 RPM
SRP017611_brain 16 .31 RPM 48 .83 RPM
SRP017611_kidney 11 .80 RPM 97 .86 RPM
SRP017611_liver 9 .97 RPM 70 .75 RPM
SRP030211_testis 15 .75 RPM 60 .75 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_1840 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1840 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1840 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 ENSBTAG00000003577 2 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 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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