RetrogeneDB ID:

retro_rnor_467

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:1:104876339..104877783(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Far1
Ensembl ID:ENSRNOG00000013176
Aliases:Far1, Mlstd2
Description:Fatty acyl-CoA reductase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q66H50]


Retrocopy-Parental alignment summary:






>retro_rnor_467
TTGCTGAGATCTTGTCCTGAGGTGAATTCAGTCTATGTTTTGGTGAGGCAAATAGCCGGACAGACACCCCAAGAATGAGT
GGAAGAAATCCTCAGTGGCAAGCTTTTCAACAGGTTGAGAGATGAAAATCCAGATTTTAGACAGAAAATTATAGCAATCA
ACAGTGAACTCACCCAACCTAAACTGGCTCAGTGAAGAAGATAAGGAGATCATTATAGATTCTACCAATGTCATATTTCA
CTGTGCAGTTACTGTAAGATTTAATGAAAATTTAAGAGATGCTGTTCAGTTAAATGTATTCGCTACATGACAGCTTATTC
TCCTTGCACAGCAAATGAAGAATCTGGAAGTGTTCATGCATGCCTCAACAGCGTACACCTACTGCAATCAAAAGCATATT
GATGAAGTAGTTTATCCATCCCCTGTAGATCCCAAGAAACTGATTGATTCCTTAGAATGGATGGTAAATAATATCACACC
AAAACTGATAGGCGACAGACCTAATATGTATATATACACCAAGGCATTGGCAGAATATGTTGTGCAACAAGAAGGAGCAA
AGCTAAATGTTGCAATTGTAAGGCCATCGATTGTTGGTGCCAGTTGGAAAGAACCTTTTCCAGGATGGACTGATAACTTT
AATGGACCAAGTGGTCTCTTCATTGCAGCAGGGAAAGGAATTCTTTGAACAATGTGTGCCTCCAACAATGCCCATGCAGA
TCTCGTTCCTGTAGATGTAGTTGTCAACATGAGACTTGCTGGAGCCTGGTATACTGGAATTAATAGACCAAGAAACACCA
TGGTGTATAATTGCACAACAGGCAGCACTAATTCTTTCCACTGGAGGGAAATTGAATACCATGTAATTTCCACTTTCAAG
AGGAATCCTCTCGAACAGGCCTTCAGATGGCCCAATGTAAATCTAACCTCAAATCACCTTTTATATCATTACTGGATTGC
TGTAAGCCATAAGACCCCAGCATTCCTGTATGATATCTACCTCAGGATGACTGGAAGAAGCCCAAGGATGATGGAAACAA
TCACTCATCTTCACAAAGCCATGGTATTCCTTGAATATTTTACAAGTAACACTTGGGTTTGGAATACTGATAATGTCAAT
ATGTTAATGAACCAGCTAAACCCTGAAGATTAAAAAGATCTTTAATATTGATATATGACAGTTACACTGTGCAGAATATA
TAGAAAACTACTGCATGGGTACTAAAAAATATGTATTGAATGAAGAGATGTCAGGCCTCCTTGTAGCTAGAAAGCATCTG
AATAAGTTGCTGAATATCTGTTATGATTTCAATACAATACTTGTGATACTTATCTGGTGCATTTTTGTTGCAAGATCACA
AATGGCAAGAAACATCTGGTGTTTTGTGGTTAGTCTGTGTTACAAATTTCTGTCAAACTTTGAGCATCCAGCACTATGAG
ATAC

ORF - retro_rnor_467 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82. %
Parental protein coverage: 94.37 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLLRSCPKVNSVYVLVRQKAGQTPQERVEEILSGKLFDRLRDENPDFRQKIIAINSELTQPKLA-LSEEDK
LLRSCP.VNSVYVLVRQ.AGQTPQE.VEEILSGKLF.RLRDENPDFRQKIIAINSELTQPKLA...E...
RetrocopyLLRSCPEVNSVYVLVRQIAGQTPQE*VEEILSGKLFNRLRDENPDFRQKIIAINSELTQPKLA>SEEDKE
ParentalEIIIDSTNVIFHCAATVRFNENLRDAVQLNVIATRQLILLAQQMKNLEVFMHVSTAYAYCNRKHIDEVVY
.II.DSTNVIFHCA.TVRFNENLRDAVQLNV.AT.QLILLAQQMKNLEVFMH.STAY.YCN.KHIDEVVY
RetrocopyIII-DSTNVIFHCAVTVRFNENLRDAVQLNVFAT*QLILLAQQMKNLEVFMHASTAYTYCNQKHIDEVVY
ParentalPPPVDPKKLIDSLEWMDDGLVNDITPKLIGDRPNTYIYTKALAEYVVQQEGAKLNVAIVRPSIVGASWKE
P.PVDPKKLIDSLEWM....VN.ITPKLIGDRPN.YIYTKALAEYVVQQEGAKLNVAIVRPSIVGASWKE
RetrocopyPSPVDPKKLIDSLEWM----VNNITPKLIGDRPNMYIYTKALAEYVVQQEGAKLNVAIVRPSIVGASWKE
ParentalPFPGWIDNFNGPSGLFIAAGKGILRTMRASNNALADLVPVDVVVNTSLAAAWYSGVNRPRNIMVYNCTTG
PFPGW.DNFNGPSGLFIAAGKGIL.TM.ASNNA.ADLVPVDVVVN..LA.AWY.G.NRPRN.MVYNCTTG
RetrocopyPFPGWTDNFNGPSGLFIAAGKGIL*TMCASNNAHADLVPVDVVVNMRLAGAWYTGINRPRNTMVYNCTTG
ParentalSTNPFHWGEVGDYLNHSFKTNPLNQVFRHPYVKFYSNNLMLHYWKGVKHTVPALLLDLALRLTGQKPWMM
STN.FHW.E........FK.NPL.Q.FR.P.V...SN.L..HYW..V.H..PA.L.D..LR.TG..P.MM
RetrocopySTNSFHWREIEYHVISTFKRNPLEQAFRWPNVNLTSNHLLYHYWIAVSHKTPAFLYDIYLRMTGRSPRMM
ParentalKTITRLHKAMVFLEYFTSNSWVWNTDNVNMLMNQLNPED-KKTFNIDVRQLHWAEYIENYCMGTKKYVLN
.TIT.LHKAMVFLEYFTSN.WVWNTDNVNMLMNQLNPED.KK.FNID..QLH.AEYIENYCMGTKKYVLN
RetrocopyETITHLHKAMVFLEYFTSNTWVWNTDNVNMLMNQLNPED>KKIFNIDI*QLHCAEYIENYCMGTKKYVLN
ParentalEEMSGLPAARKHLNKLRNIRYGFNTILVILIWRIFIARSQMARNIWYFVVSLCYKFLSYFR-ASSTMRY
EEMSGL..ARKHLNKL.NI.Y.FNTILVILIW.IF.ARSQMARNIW.FVVSLCYKFLS.F..ASSTMRY
RetrocopyEEMSGLLVARKHLNKLLNICYDFNTILVILIWCIFVARSQMARNIWCFVVSLCYKFLSNFE<ASSTMRY

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 .29 RPM 26 .89 RPM
SRP017611_kidney 0 .00 RPM 19 .61 RPM
SRP017611_liver 0 .00 RPM 1 .41 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_467 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_467 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_467 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000034902 retrocopies
retro_chof_1358, retro_chof_1733,
Callithrix jacchus ENSCJAG000000100771 retrocopy
retro_cjac_545,
Cavia porcellus ENSCPOG000000026541 retrocopy
retro_cpor_267,
Homo sapiens ENSG000001976011 retrocopy
retro_hsap_1225,
Gorilla gorilla ENSGGOG000000011801 retrocopy
retro_ggor_958,
Macaca mulatta ENSMMUG000000119901 retrocopy
retro_mmul_1301,
Nomascus leucogenys ENSNLEG000000176951 retrocopy
retro_nleu_698,
Oryctolagus cuniculus ENSOCUG000000043362 retrocopies
retro_ocun_1056, retro_ocun_790,
Otolemur garnettii ENSOGAG000000050642 retrocopies
retro_ogar_1353, retro_ogar_341,
Pongo abelii ENSPPYG000000034701 retrocopy
retro_pabe_1019,
Pan troglodytes ENSPTRG000000241901 retrocopy
retro_ptro_840,
Rattus norvegicus ENSRNOG00000013176 1 retrocopy
retro_rnor_467 ,


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