RetrogeneDB ID:

retro_rnor_59

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:1:205713406..205714402(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000048397
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Sephs1
Ensembl ID:ENSRNOG00000018125
Aliases:None
Description:selenide, water dikinase 1 [Source:RefSeq peptide;Acc:NP_001098100]


Retrocopy-Parental alignment summary:






>retro_rnor_59
ATGGACTCCTGCGTCATCCCCCTGAGGCACGGAGGCCTGTCGCTGGTGCAGACCACCGACTTCTTTTACCCCTTGGTGGA
AGATCCCTATATGATGGGGCGCATAGCTTGTGCCAATGTGCTCAGTGACCTCTATGCCATGGGCATTACCGAGTGTGACA
ACATGTTGATGTTACTCAGTGTGAGCCAGAGCATGAGTGAAAAGGAACGAGAGAAGGTAACGCCGCTCATGATCAAAGGC
TTTCGTGACGCTGCGGAAGAGGGAGGAACTGCAGTGACTGGTGGACAGACAGTGGTCAACCCTTGGATTATCATCGGTGG
GGTTGCCACTGTGGTGTGTCAGCAAAATGAATTCATAATGCCTGACAGCGCTGTGGTAGGAGATGTGCTGGTATTAACCA
AGCCTTTAGGAACCCAGGTTGCTGCCAATGCCCACCAATGGCTGGATAATCCTGAGAAATGGAATAAAATCAAGATGGTG
GTTTCCAGAGAGGAAGTAGAGCTAGCCTATCAGGAAGCTATGTTCAACATGGCTACTCTGAACAGGACTGCTGCTAGCTT
GATGCACACTTTTAATGCTCACGCAGCCACGGATATCACAGGCTTTGGCATATTAGGACACTCCCAGAACCTCGCAAAAC
AGCAAAAAAATGAAGTGTCCTTTGTCATTCACAATCTGCCAATCATTGCCAAGATGGCTGCGATCAGCAAAGCCAGTGGG
CGCTTTGGCCTCCTCCAAGGAACATCAGCTGAAACCTCTGGGGGATTACTGATCTGTCTGCCAAGAGAACAGGCGGCCCG
CTTTTGTTCGGAAATCAAATCTTCCAAGTACGGAGAGGGTCACCAAGCTTGGATTGTTGGCATCGTGGAGAAGGGAAACC
GGACAGCCCGGATCATTGACAAGCCTCGCGTTATTGAAGTTCTACCTCGGGGAGCCTCTGCTTCTGCTGCTGCTGCTCCT
GACAATTCCAATGCAGCCTCTGAGCCTAGTTCTTGA

ORF - retro_rnor_59 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.37 %
Parental protein coverage: 81.89 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRER
MD.CVIPLRHGGLSLVQTTD..YP.V.DPYMMGRIACANVLSDLYAMG.TECDNMLMLL.VS..M...ER
RetrocopyMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMSEKER
ParentalDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQV
.KV.PL.I.GF.DAAEE.GT.VTGGQTV.NPWI..GGVAT.VCQ.NEFIMPD.AV.GDVLVLTKPLGTQV
RetrocopyEKVTPLMIKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQQNEFIMPDSAVVGDVLVLTKPLGTQV
ParentalAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMVNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQN
A...HQWLD.PEKWNKIK.VV..E.VELAYQEAM.NMA.LNRTAA.LMHTFNAHAATDITGFGILGH.QN
RetrocopyAANAHQWLDNPEKWNKIKMVVSREEVELAYQEAMFNMATLNRTAASLMHTFNAHAATDITGFGILGHSQN
ParentalLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGE
LAKQQ.NEVSFVIHNLP..AKMAA.SKA.G..FGL..GT..ETSGGLLICLPREQAARFC.EIKS.KYGE
RetrocopyLAKQQKNEVSFVIHNLPIIAKMAAISKASGR-FGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGE
ParentalGHQAWIIGIVEKGNRTARIIDKPRIIEVAPQVATQNVNPTP
GHQAWI.GIVEKGNRTARIIDKPR.IEV.P..A.......P
RetrocopyGHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGASASAAAAP

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 25 .45 RPM 29 .77 RPM
SRP017611_kidney 82 .69 RPM 80 .53 RPM
SRP017611_liver 97 .76 RPM 38 .86 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_59 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_59 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_59 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000135551 retrocopy
retro_amel_21,
Canis familiaris ENSCAFG000000047432 retrocopies
retro_cfam_1787, retro_cfam_250,
Callithrix jacchus ENSCJAG000000094942 retrocopies
retro_cjac_166, retro_cjac_2219,
Dipodomys ordii ENSDORG000000141191 retrocopy
retro_dord_792,
Equus caballus ENSECAG000000142811 retrocopy
retro_ecab_77,
Felis catus ENSFCAG000000039211 retrocopy
retro_fcat_96,
Homo sapiens ENSG000000864753 retrocopies
retro_hsap_2196, retro_hsap_3860, retro_hsap_4705,
Gorilla gorilla ENSGGOG000000038062 retrocopies
retro_ggor_147, retro_ggor_2924,
Loxodonta africana ENSLAFG000000046701 retrocopy
retro_lafr_125,
Macropus eugenii ENSMEUG000000121881 retrocopy
retro_meug_245,
Myotis lucifugus ENSMLUG000000019712 retrocopies
retro_mluc_2350, retro_mluc_728,
Macaca mulatta ENSMMUG000000212334 retrocopies
retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Monodelphis domestica ENSMODG000000168641 retrocopy
retro_mdom_86,
Mustela putorius furoENSMPUG000000009481 retrocopy
retro_mputfur_20,
Mus musculus ENSMUSG000000266621 retrocopy
retro_mmus_248,
Nomascus leucogenys ENSNLEG000000122057 retrocopies
retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Otolemur garnettii ENSOGAG000000078071 retrocopy
retro_ogar_3026,
Ochotona princeps ENSOPRG000000065873 retrocopies
retro_opri_271, retro_opri_655, retro_opri_670,
Procavia capensis ENSPCAG000000156171 retrocopy
retro_pcap_341,
Pongo abelii ENSPPYG000000020996 retrocopies
retro_pabe_1324, retro_pabe_1378, retro_pabe_2074, retro_pabe_2620, retro_pabe_3047, retro_pabe_3652,
Pan troglodytes ENSPTRG000000023033 retrocopies
retro_ptro_1135, retro_ptro_1669, retro_ptro_3126,
Pteropus vampyrus ENSPVAG000000029452 retrocopies
retro_pvam_115, retro_pvam_566,
Rattus norvegicus ENSRNOG00000018125 1 retrocopy
retro_rnor_59 ,
Tursiops truncatus ENSTTRG000000111141 retrocopy
retro_ttru_649,


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