RetrogeneDB ID:

retro_rnor_6

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:13:40669575..40670628(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000047257
Aliases:Tmem185b, RGD1309602
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Tmem185a
Ensembl ID:ENSRNOG00000011047
Aliases:Tmem185a, RGD1563037
Description:transmembrane protein 185-like [Source:RefSeq peptide;Acc:NP_001129184]


Retrocopy-Parental alignment summary:






>retro_rnor_6
ATGAACCCCAGGGGCCTGTTCCAGGACTTCAACCCCAGTAAGTTCCTCATTTATGCCTGCTTGCTGCTCTTCTCCGTGCT
GCTGCCCCTGCGTCTGGACGGCATCATCCAGTGGAGCTACTGGGCGGTCTTCGCCCCCATCTGGCTGTGGAAGCTCCTGG
TCATCGTGGGCGCCTCGGTGGGTGCGGGCGTGTGGGCCCGCAACCCTCGCTACCGTACGGAGGGGGAAGCCTGTGTGGAA
TTCAAAGCCATGCTGATCGCTGTGGGCATCCACCTGCTGCTGCTCATGTTTGAGATTCTAGTCTGCGACCGGGTGGAGAG
GGGAACCCACTTTTGGCTGCTGGTCTTCATGCCACTCTTCTTCGTTTCCCCGGTGTCCGTGGCCGCCTGCGTCTGGGGCT
TCCGACATGACAGGTCTTTGGAACTGGAAATCCTGTGCTCCGTCAACATCCTGCAGTTTATCTTCATCGCTCTGAGGTTG
GACAGGATTATCCACTGGCCGTGGCTGGTGGTATTCGTGCCTCTGTGGATCCTCATGTCATTCCTCTGCCTGGTGGTTCT
CTATTACATCGTGTGGTCCCTCCTGTTCCTGCGGTCCCTGGATGTGGTTGCAGAGCAGCGAAGAACACATGTGACCATGG
CCATCAGCTGGATCACGATTGTCGTGCCCCTGCTCACCTTTGAGGTCCTGCTAGTTCACAGACTGGATGGCCACAATACG
TTCTCTTACATTTCCATATTCACCCCTCTTTGGCTGTCATTACTGACTTTGATGGCCACGACGTTCAGGCGGAAAGGGGG
CAATCATTGGTGGTTCGGTATTCGCAGGGATTTCTGTCAGTTTCTACTTGAGGTTTTCCCGTTTTTAAGAGAATATGGGA
ATATCTCTTACGATCTCCATCACGAAGACAGCGAAGATGCTGAAGACGCGTCGGCGTTAGAAGCTCCGAAAATTGCCCCA
ATGTTTGGAAAGAAGGCCCGGGTAGTTATAACACAGAGCCCTGGGAAATACGTCCCTCCACCTCCCAAGTTAAACATTGA
TATGCCAGACTAA

ORF - retro_rnor_6 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.57 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMNLRGLFQDFNPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQ
MN.RGLFQDFNPSKFLIYACLLLFSVLL.LRLDGIIQWSYWAVFAPIWLWKL.VIVGASVG.GVWARNP.
RetrocopyMNPRGLFQDFNPSKFLIYACLLLFSVLLPLRLDGIIQWSYWAVFAPIWLWKLLVIVGASVGAGVWARNPR
ParentalYRAEGETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
YR.EGE.CVEFKAMLIAVGIHLLLLMFE.LVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
RetrocopyYRTEGEACVEFKAMLIAVGIHLLLLMFEILVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
ParentalELEILCSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTH
ELEILCSVNILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH
RetrocopyELEILCSVNILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTH
ParentalITMALSWMTIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQ
.TMA.SW.TIVVPLLTFE.LLVH.LDGHN.FS.I.IF.PLWLSL.TLMATTF..KGGNHWWFGIR.DFCQ
RetrocopyVTMAISWITIVVPLLTFEVLLVHRLDGHNTFSYISIFTPLWLSLLTLMATTFRRKGGNHWWFGIRRDFCQ
ParentalFLLEIFPFLREYGNISYDLHHEDSEETEETPVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
FLLE.FPFLREYGNISYDLHHEDSE..E.....E.PKIAPMF.KKARVVITQSPGKYV.PPPKLNI.MPD
RetrocopyFLLEVFPFLREYGNISYDLHHEDSEDAEDASALEAPKIAPMFGKKARVVITQSPGKYVPPPPKLNIDMPD

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 12 .80 RPM 16 .32 RPM
SRP017611_kidney 31 .19 RPM 30 .43 RPM
SRP017611_liver 4 .30 RPM 16 .27 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_rnor_6 retrocopy
EST ID Start End Identity Match Mis-match Score
CB713808 40669860 40670275 99.1 400 3 395

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_6 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_6 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_104
Gorilla gorilla retro_ggor_189
Pongo abelii retro_pabe_118
Macaca mulatta retro_mmul_310
Mus musculus retro_mmus_358
Parental genes homology:
Parental genes homology involve 26 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086371 retrocopy
retro_acar_65,
Ailuropoda melanoleuca ENSAMEG000000093511 retrocopy
retro_amel_8,
Bos taurus ENSBTAG000000068181 retrocopy
retro_btau_1,
Canis familiaris ENSCAFG000000191031 retrocopy
retro_cfam_159,
Cavia porcellus ENSCPOG000000036221 retrocopy
retro_cpor_5,
Dasypus novemcinctus ENSDNOG000000118641 retrocopy
retro_dnov_2451,
Dipodomys ordii ENSDORG000000150271 retrocopy
retro_dord_67,
Equus caballus ENSECAG000000093991 retrocopy
retro_ecab_426,
Felis catus ENSFCAG000000244831 retrocopy
retro_fcat_1116,
Homo sapiens ENSG000001559841 retrocopy
retro_hsap_104,
Gorilla gorilla ENSGGOG000000242681 retrocopy
retro_ggor_189,
Loxodonta africana ENSLAFG000000030441 retrocopy
retro_lafr_898,
Microcebus murinus ENSMICG000000046391 retrocopy
retro_mmur_106,
Myotis lucifugus ENSMLUG000000013191 retrocopy
retro_mluc_2075,
Macaca mulatta ENSMMUG000000028881 retrocopy
retro_mmul_310,
Mustela putorius furoENSMPUG000000118961 retrocopy
retro_mputfur_46,
Mus musculus ENSMUSG000000731391 retrocopy
retro_mmus_358,
Nomascus leucogenys ENSNLEG000000134871 retrocopy
retro_nleu_2723,
Otolemur garnettii ENSOGAG000000164141 retrocopy
retro_ogar_88,
Procavia capensis ENSPCAG000000091601 retrocopy
retro_pcap_260,
Pongo abelii ENSPPYG000000208091 retrocopy
retro_pabe_118,
Pteropus vampyrus ENSPVAG000000138221 retrocopy
retro_pvam_30,
Rattus norvegicus ENSRNOG00000011047 1 retrocopy
retro_rnor_6 ,
Sus scrofa ENSSSCG000000127391 retrocopy
retro_sscr_494,
Ictidomys tridecemlineatus ENSSTOG000000144841 retrocopy
retro_itri_8,
Tursiops truncatus ENSTTRG000000006431 retrocopy
retro_ttru_868,


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