RetrogeneDB ID:

retro_rnor_2518

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:7:42011791..42013189(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Cs
Ensembl ID:ENSRNOG00000023520
Aliases:None
Description:citrate synthase, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_570111]


Retrocopy-Parental alignment summary:






>retro_rnor_2518
ATGGCTCTACTCATTGAGGCAGCCCGACTCTTGGGAGCCAAGAATCCATCCTGTCTGATCTTTGCTGCCCGGCACTCCAG
TGCTTCTTCCACGAATTTGAAAGACGTACTGAGCAGTCTGATACCTAAGGAGCAAGCCAGAATTAAGACCTTCAGAGAGC
AACATGGGAAGACAGTGATGGGCCAAATCACTGTGGACATGATGTCCGGTGGCATGAGAGGCATGAAGAGACTTGTGTAT
GAGACATCGGTTCTTGATCCTGATGAGGGCATCCGTTTATGAGGCCATAGTGTCCCTGAATGCCAGAAACTGCTGCCTAA
GGCTAAGGGTGGGGAGGAACCCTTGCCTGAGGGCTTATTTTGGCTGCTGGTAACTGGACAGATGCCCACAGAGGAACAGG
TATCCTGGCTCTCACAAGAATGGGCCAAAAGGGCAGTTCTGCCTTCTCTTGTGGTCACCATGTTGGACAATTTTCCAACC
AATCTACACCCCATGTCTCAGCTCAGTGCAGCCATCACAGCCCTCAACAATGAAAGCTACTTTGCCCGGGCATATGCAGA
GGGAATGAGCCAAACCAAGTACTGGGAACTCATCTATGAAGACTGCATGGACCTGATTGCCAAGTTACCGTGTGTTGCAA
CAAAGATCTACCGGAATCTGTACCGGGAGGACACCAGTATTGAAGCCATTGTCCCTAAACTGGACTGGTCCCATAATTTT
ACCAACATGTTAGGCTTCATGGACCCTCAATTCACTGAGCTCATGCATTTGTATCTCACCATCCACAGTGACCACGAGGG
TGGTAACGTAAGTGCCCACACAAGCCATTTGGTGGGCAGTGCCCTTTCAGACCCTTACCTGTCCTTAGCAGCAGCCATGA
GTGGGCTGGCCTGACCGCTCCATGGACTAGCGAATCAGGAGGTGCTTGTCTGGCTGACCAAGCTACAGAAGGAAGTTGGC
AAAGATGTGTCAGATGAGAAGTTACGTGACTACATCTGGAACACACTCAACTCAGTGCAGGTTGTCCCAGGATATGGTCA
TTCTGTACTAAGGAAGACTGATCCACGATATTCCTGTCAGCGAGAGTTTGCTCTGAAACACCTGCCTAAGGATCCCATGT
TTAAGCTGGTTGTTCAGCTGTACAAGATTGTGCCCAGTATCCTCTTAGAGCAAGGAAAGGCTAAGAACCCCTGGCCCAAC
GTAGATGCTCACAGTGGAGTGCTGCTTCAGCACTACGGCATGACGGAGATGAATTACTACACAGTCCTGTTTGGAGTGTC
GAGGGCACTGGGTGTGCTAGCCCAGCTCATCTGGAGCAGAGCCCTAGGCTTCCCTCTAGAAAACCCCAAGTCCATGAGCA
CAGATGGTCTGATAAAGTTTGTGGACTCTAAGTCAGGG

ORF - retro_rnor_2518 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.13 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 2
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMALLTAAARLLGAKNSSCLVLAARHASASSTNLKDILSNLIPKEQARVKTFRQQHGKTVVGQITVDMMYG
MALL..AARLLGAKN.SCL..AARH.SASSTNLKD.LS.LIPKEQAR.KTFR.QHGKTV.GQITVDMM.G
RetrocopyMALLIEAARLLGAKNPSCLIFAARHSSASSTNLKDVLSSLIPKEQARIKTFREQHGKTVMGQITVDMMSG
ParentalGMRGMKGLVYETSVLDPDEGIRFRGYSIPECQKLLPKAKGGEEPLPEGLFWLLVTGQMPTEEQVSWLSQE
GMRGMK.LVYETSVLDPDEGIR..G.S.PECQKLLPKAKGGEEPLPEGLFWLLVTGQMPTEEQVSWLSQE
RetrocopyGMRGMKRLVYETSVLDPDEGIRL*GHSVPECQKLLPKAKGGEEPLPEGLFWLLVTGQMPTEEQVSWLSQE
ParentalWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAITALNSESNFARAYAEGINRTKYWELIYEDCMDLIAKLP
WAKRA.LPS.VVTMLDNFPTNLHPMSQLSAAITALN.ES.FARAYAEG...TKYWELIYEDCMDLIAKLP
RetrocopyWAKRAVLPSLVVTMLDNFPTNLHPMSQLSAAITALNNESYFARAYAEGMSQTKYWELIYEDCMDLIAKLP
ParentalCVAAKIYRNLYREGSSIGAIDSKLDWSHNFTNMLGYTEPQFTELMRLYLTIHSDHEGGNVSAHTSHLVGS
CVA.KIYRNLYRE..SI.AI..KLDWSHNFTNMLG...PQFTELM.LYLTIHSDHEGGNVSAHTSHLVGS
RetrocopyCVATKIYRNLYREDTSIEAIVPKLDWSHNFTNMLGFMDPQFTELMHLYLTIHSDHEGGNVSAHTSHLVGS
ParentalALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVPGYGHAVL
ALSDPYLS.AAAM.GLA.PLHGLANQEVLVWLT.LQKEVGKDVSDEKLRDYIWNTLNS..VVPGYGH.VL
RetrocopyALSDPYLSLAAAMSGLA*PLHGLANQEVLVWLTKLQKEVGKDVSDEKLRDYIWNTLNSVQVVPGYGHSVL
ParentalRKTDPRYSCQREFALKHLPKDPMFKLVAQLYKIVPNILLEQGKAKNPWPNVDAHSGVLLQYYGMTEMNYY
RKTDPRYSCQREFALKHLPKDPMFKLV.QLYKIVP.ILLEQGKAKNPWPNVDAHSGVLLQ.YGMTEMNYY
RetrocopyRKTDPRYSCQREFALKHLPKDPMFKLVVQLYKIVPSILLEQGKAKNPWPNVDAHSGVLLQHYGMTEMNYY
ParentalTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTDGLMKFVDSKSG
TVLFGVSRALGVLAQLIWSRALGFPLE.PKSMSTDGL.KFVDSKSG
RetrocopyTVLFGVSRALGVLAQLIWSRALGFPLENPKSMSTDGLIKFVDSKSG

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 0 .00 RPM 152 .28 RPM
SRP017611_kidney 0 .00 RPM 146 .05 RPM
SRP017611_liver 0 .00 RPM 39 .47 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_2518 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_2518 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2518 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Mus musculus retro_mmus_258
Parental genes homology:
Parental genes homology involve 21 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000043711 retrocopy
retro_btau_386,
Canis familiaris ENSCAFG000000001151 retrocopy
retro_cfam_765,
Choloepus hoffmanni ENSCHOG000000003971 retrocopy
retro_chof_1803,
Callithrix jacchus ENSCJAG000000112751 retrocopy
retro_cjac_2031,
Dasypus novemcinctus ENSDNOG000000109072 retrocopies
retro_dnov_205, retro_dnov_468,
Echinops telfairi ENSETEG000000120351 retrocopy
retro_etel_584,
Homo sapiens ENSG000000624852 retrocopies
retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla ENSGGOG000000090962 retrocopies
retro_ggor_1432, retro_ggor_2445,
Macropus eugenii ENSMEUG000000056572 retrocopies
retro_meug_1078, retro_meug_1304,
Microcebus murinus ENSMICG000000176592 retrocopies
retro_mmur_1322, retro_mmur_394,
Macaca mulatta ENSMMUG000000024832 retrocopies
retro_mmul_1502, retro_mmul_1840,
Mus musculus ENSMUSG000000056831 retrocopy
retro_mmus_258,
Nomascus leucogenys ENSNLEG000000175142 retrocopies
retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus ENSOCUG000000072161 retrocopy
retro_ocun_1183,
Pongo abelii ENSPPYG000000046541 retrocopy
retro_pabe_2972,
Rattus norvegicus ENSRNOG00000023520 1 retrocopy
retro_rnor_2518 ,
Sorex araneus ENSSARG000000100932 retrocopies
retro_sara_360, retro_sara_628,
Sus scrofa ENSSSCG000000210911 retrocopy
retro_sscr_321,
Sus scrofa ENSSSCG000000228581 retrocopy
retro_sscr_322,
Tupaia belangeri ENSTBEG000000064251 retrocopy
retro_tbel_4652,
Tarsius syrichta ENSTSYG000000044831 retrocopy
retro_tsyr_1659,


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