RetrogeneDB ID:

retro_rnor_2453

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:7:41342693..41344067(+)
Located in intron of:ENSRNOG00000024450
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Galnt12
Ensembl ID:ENSRNOG00000008099
Aliases:Galnt12, RGD1562001
Description:None


Retrocopy-Parental alignment summary:






>retro_rnor_2453
CAGCCTCTTTATAAAAAGCCCCCTGCAGATTCCCATGCTCTTGGGGAATGGGGGAGAGCAAGCAAACTCCAGCTCGATGA
GGGTGAACTGAAGCAGCAAGAAGAACTCATTGAGAGATACGCCATCAACATTTACCTCAGTGACAGGATCTCCCTGCACC
GCCACATAGAGGATAAAAGAATGTATGAGTGTAAAGCCAAGAAGTTCCACTACAGGTCGCTCCCCACCACCTCCGTTATC
ATCGCCTTTTATAATGAAGCCTGGTCCACTCTGCTTCGAACCATTCACAGTGTTCTAGAAACTTCTCCAGCTGTGCTTTT
AAAGGAGATCATCTTGGTGGATGACTTAAGTGACAGAATTTATCTGAAGGCTCAACTTGAAGCTTATATCAGCAACCTCG
ATAGAGTTCGCTTGATTAGAACCAATAAGAGAGAGGGGCTGGTCCGGGCCCGTCTGATTGGGGCCACTTTTGCCACCGGG
GATGTCCTCACTTTCCTGGATTGTCACTGTGAGTGTAACACTGGTTGGTTGGAACCGCTTTTGGAAAGGATCAGTAGAGA
TGAAACAGCAATTGTATGTCCTGTCATCGACACCATCGACTGGAATACTTTCGAATTCTATATGCAGACCGGGGAGCCCA
TGATTGGTGGTTTTGACTGGCGTTTGACCTTCCAGTGGCATTCTGTCCCCAAACATGAAAGGGACAGGCGGACATCAAGA
ATTGACCCCATCAGGTCACCCACCATGGCAGGAGGCCTGTTTGCTGTCAGCAAGAAGTATTTTCAGTACCTGGGAACGTA
TGACACTGGCATGGAAGTCTGGGGAGGTGAAAACCTTGAGCTGTCTTTCAGGGTTTGGCAGTGCGGCGGCAAGCTGGAGA
TCCACCCATGTTCTCACGTGGGCCACGTGTTTCCCAAGCGGGCGCCCTACGCTCGCCCCAACTTCCTACAGAACACCGCT
AGGGCGGCGGAAGTGTGGATGGATGACTACAAAGAGCATTTCTATAACCGGAACCCTCCCGCTCGAAAAGAGACCTATGG
CGATATTTCGGAAAGGAAGTTACTGAGGGAACGGCTGCAATGTAAGAGCTTCGACTGGTATTTGAAAAATGTGTTCTCTA
ACTTACACGTTCCGGAGGATAGACCTGGCTGGCACGGAGCCATCCGCAGTATGGGCATCTCTTCAGAGTGCTTAGATTAT
AATGCACCGGACAACAACCCTACGGGTGCTAACCTTTCGCTGTTTGGATGCCACGGTCAAGGGGGCAATCAGTTCTTTGA
ATATACTTCAAACAAGGAAATCAGATTTAATTCCGTGACGGAATTATGTGCAGAGGTCCCCCAACAAAAGGATTATGTAG
GGATGCAAAACTGC

ORF - retro_rnor_2453 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.83 %
Parental protein coverage: 80.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalEPVLPRPPLPADALGAKGEAVRLQLQGEELRLQEESVQRHQINIYLSDRISLHRRLPERWNPLCREVKYD
.P....PP....ALG..G.A..LQL...EL..QEE...R..INIYLSDRISLHR.........C...K..
RetrocopyQPLYKKPPADSHALGEWGRASKLQLDEGELKQQEELIERYAINIYLSDRISLHRHIEDKRMYECKAKKFH
ParentalYDNLPKTSVVIAFYNEAWSTLLRTVYSVLETSPDILLEEVILVDDYSDREHLKEPLANELSQLPKVRLIR
Y..LP.TSV.IAFYNEAWSTLLRT..SVLETSP..LL.E.ILVDD.SDR..LK..L....S.L..VRLIR
RetrocopyYRSLPTTSVIIAFYNEAWSTLLRTIHSVLETSPAVLLKEIILVDDLSDRIYLKAQLEAYISNLDRVRLIR
ParentalASKREGLVRARLLGASAARGEVLTFLDCHCECHEGWLEPLLQRIHEKESAVVCPVIDVIDWNTFEYLGNS
..KREGLVRARL.GA..A.G.VLTFLDCHCEC..GWLEPLL.RI...E.A.VCPVID.IDWNTFE.....
RetrocopyTNKREGLVRARLIGATFATGDVLTFLDCHCECNTGWLEPLLERISRDETAIVCPVIDTIDWNTFEFYMQT
ParentalGEPQIGGFDWRLVFTWHVVPQRERKLMRSPIDVIRSPTMAGGLFAVSKRYFEYLGSYDTGMEVWGGENLE
GEP.IGGFDWRL.F.WH.VP..ER....S.ID.IRSPTMAGGLFAVSK.YF.YLG.YDTGMEVWGGENLE
RetrocopyGEPMIGGFDWRLTFQWHSVPKHERDRRTSRIDPIRSPTMAGGLFAVSKKYFQYLGTYDTGMEVWGGENLE
ParentalFSFRIWQCGGTLETHPCSHVGHVFPKQAPYSRSKALANSVRAAEVWMDDFKELYYHRNPQARLEPFGDVT
.SFR.WQCGG.LE.HPCSHVGHVFPK.APY.R...L.N..RAAEVWMDD.KE..Y.RNP.AR.E..GD..
RetrocopyLSFRVWQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDDYKEHFYNRNPPARKETYGDIS
ParentalERKKLRAKLQCKDFKWFLDTVYPELHVPEDRPGFFGMLENRGLRGYCLDYNPPSENNVEGHQVLLYLCHG
ERK.LR..LQCK.F.W.L..V...LHVPEDRPG..G.....G....CLDYN.P..NN..G....L..CHG
RetrocopyERKLLRERLQCKSFDWYLKNVFSNLHVPEDRPGWHGAIRSMGISSECLDYNAP-DNNPTGANLSLFGCHG
ParentalMGQNQFFEYTSRQEIRYNTRQPEACIAVEEGKDVLIMDLC
.G.NQFFEYTS..EIR.N....E.C..V...KD...M..C
RetrocopyQGGNQFFEYTSNKEIRFNS-VTELCAEVPQQKDYVGMQNC

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 .43 RPM 1 .01 RPM
SRP017611_kidney 4 .47 RPM 6 .14 RPM
SRP017611_liver 4 .57 RPM 0 .40 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_2453 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_2453 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2453 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_777
Gorilla gorilla retro_ggor_890
Pongo abelii retro_pabe_949
Macaca mulatta retro_mmul_888
Mus musculus retro_mmus_183
Oryctolagus cuniculus retro_ocun_1260
Bos taurus retro_btau_1410
Equus caballus retro_ecab_52
Parental genes homology:
Parental genes homology involve 33 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000023021 retrocopy
retro_acar_54,
Ailuropoda melanoleuca ENSAMEG000000045201 retrocopy
retro_amel_93,
Anas platyrhynchos ENSAPLG000000121971 retrocopy
retro_apla_8,
Bos taurus ENSBTAG000000090371 retrocopy
retro_btau_1410,
Canis familiaris ENSCAFG000000024941 retrocopy
retro_cfam_683,
Cavia porcellus ENSCPOG000000124181 retrocopy
retro_cpor_1467,
Equus caballus ENSECAG000000165461 retrocopy
retro_ecab_52,
Ficedula albicollis ENSFALG000000051881 retrocopy
retro_falb_8,
Felis catus ENSFCAG000000088311 retrocopy
retro_fcat_126,
Gorilla gorilla ENSGGOG000000057921 retrocopy
retro_ggor_890,
Loxodonta africana ENSLAFG000000220111 retrocopy
retro_lafr_536,
Meleagris gallopavo ENSMGAG000000072441 retrocopy
retro_mgal_1,
Microcebus murinus ENSMICG000000110751 retrocopy
retro_mmur_282,
Myotis lucifugus ENSMLUG000000026301 retrocopy
retro_mluc_804,
Macaca mulatta ENSMMUG000000195611 retrocopy
retro_mmul_888,
Mustela putorius furoENSMPUG000000065021 retrocopy
retro_mputfur_569,
Mus musculus ENSMUSG000000397741 retrocopy
retro_mmus_183,
Nomascus leucogenys ENSNLEG000000170191 retrocopy
retro_nleu_940,
Oryctolagus cuniculus ENSOCUG000000162211 retrocopy
retro_ocun_1260,
Otolemur garnettii ENSOGAG000000014082 retrocopies
retro_ogar_3253, retro_ogar_717,
Ochotona princeps ENSOPRG000000060292 retrocopies
retro_opri_121, retro_opri_515,
Procavia capensis ENSPCAG000000050681 retrocopy
retro_pcap_63,
Pongo abelii ENSPPYG000000194371 retrocopy
retro_pabe_949,
Pelodiscus sinensis ENSPSIG000000172461 retrocopy
retro_psin_1,
Pan troglodytes ENSPTRG000000211801 retrocopy
retro_ptro_777,
Pteropus vampyrus ENSPVAG000000087741 retrocopy
retro_pvam_1347,
Rattus norvegicus ENSRNOG00000008099 3 retrocopies
retro_rnor_1084, retro_rnor_1085, retro_rnor_2453 ,
Sarcophilus harrisii ENSSHAG000000174741 retrocopy
retro_shar_44,
Sus scrofa ENSSSCG000000053791 retrocopy
retro_sscr_32,
Ictidomys tridecemlineatus ENSSTOG000000213061 retrocopy
retro_itri_41,
Tupaia belangeri ENSTBEG000000036271 retrocopy
retro_tbel_2065,
Tarsius syrichta ENSTSYG000000049751 retrocopy
retro_tsyr_386,
Tursiops truncatus ENSTTRG000000108481 retrocopy
retro_ttru_212,


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