RetrogeneDB ID:

retro_rnor_1050

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:14:51644600..51645477(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000011069
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Amd1
Ensembl ID:ENSRNOG00000000585
Aliases:Amd1, Amd1a, Amd1b
Description:S-adenosylmethionine decarboxylase proenzyme S-adenosylmethionine decarboxylase alpha chain S-adenosylmethionine decarboxylase beta chain [Source:UniProtKB/Swiss-Prot;Acc:P17708]


Retrocopy-Parental alignment summary:






>retro_rnor_1050
AAGTGGGATGTTGTTTTGAAGGATATTCAGTGCTCAACCATAAGTGTGACAAAGACTGACAAGTAGGAAGCTAAAGTACT
CAGTGAAAATAGCATGTTTTCTCAAGAGACGTTTCATTTTGAAGACATGTGGTACCACCCTCTTACTGAAAGCACTGGTT
TCCCTGTTGCAGCTTGCTAGGGACCACAGTAGATTTGACTCAATTCAAAGCTTCTTTTATTCTCATAAGAATTTCATGAA
GCCTTCTGACCAAGGGTACCCACACCAGAATTTCCAGGAAGAAATCAAGTTTCTTAATCCATTTTTCCATAATGGAGCAG
CATATTGTATGGGATGTATGAATTCTGGATGTTGGTACTTGAATACTTTGGCTCTCCCAGAAAGCCGAGTAATCAATCAG
CCAATCAAACTCTGGAAATTCTGGTAAGTGAGCTTGATTCAGCAGTTATGGACCAATTCTTCATGGAAGATGGCGTTACT
GCAAAGGATGTCACTCATGGGAGTGGAATTAGTGACCTGATACCAGATTCTGTCATTGATGCCACACTGTTCAATCCTTG
TGACTACTCAATGAATGAAATGAAATTGGATGGAACATATTGGATTATTCACATTACTCCAGAACCAGAATTTTCTTATG
TTAGCTTTGAAACAAACCTAAGTCAGACCTCCTATGACGACCTGATCAGGAAAGTTGTGGACGTCTTCAAGCCAGGAAAA
TTTGTGACCACCTTGTTTGTCAATCAGAGTTCTAAGTGTCACACAGTGCTTTCTTTGCCCCAGAATATTGACGGTTTCAA
ACGTCTTGATTGCCAGAGTTCAAAACGATTACAATTCTGTTTTTACCAGTTTTTCTAAGAAACAGCAACAACAGAGT

ORF - retro_rnor_1050 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.87 %
Parental protein coverage: 88.59 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEWDVLLKDVQCSIISVTKTDKQEAYVLSESSM-FVSKRRFILKTCGTTLLLKALVPLLKLARDYSGFDSI
.WDV.LKD.QCS.ISVTKTDK.EA.VLSE.SM.F...R.FILKTCGTTLLLKALV.LL.LARD.S.FDSI
RetrocopyKWDVVLKDIQCSTISVTKTDK*EAKVLSENSM>FLKRR-FILKTCGTTLLLKALVSLLQLARDHSRFDSI
ParentalQSFFYSRKNFMKPSHQGYPHRNFQEEIEFLNAIFPNGAAYCMGRMNSDCWYLYTLDLPESRVINQP-DQT
QSFFYS.KNFMKPS.QGYPH.NFQEEI.FLN..F.NGAAYCMG.MNS.CWYL.TL.LPESRVINQP..QT
RetrocopyQSFFYSHKNFMKPSDQGYPHQNFQEEIKFLNPFFHNGAAYCMGCMNSGCWYLNTLALPESRVINQP<NQT
ParentalLEILMSELDPAVMDQFYMKDGVTAKDVTRESGIRDLIPGSVIDATLFNPCGYSMNGMKSDGTYWTIHITP
LEIL.SELD.AVMDQF.M.DGVTAKDVT..SGI.DLIP.SVIDATLFNPC.YSMN.MK.DGTYW.IHITP
RetrocopyLEILVSELDSAVMDQFFMEDGVTAKDVTHGSGISDLIPDSVIDATLFNPCDYSMNEMKLDGTYWIIHITP
ParentalEPEFSYVSFETNLSQTSYDDLIRKVVEVFKPGKFVTTLFVNQSSKCRTVLSSPQKIDGFKRLDCQSAMFN
EPEFSYVSFETNLSQTSYDDLIRKVV.VFKPGKFVTTLFVNQSSKC.TVLS.PQ.IDGFKRLDCQS....
RetrocopyEPEFSYVSFETNLSQTSYDDLIRKVVDVFKPGKFVTTLFVNQSSKCHTVLSLPQNIDGFKRLDCQSS--K
ParentalDYNFVFTSF-AKKQQQQS
...F.F..F..KKQQQQS
RetrocopyRLQFCFYQF>SKKQQQQS

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 118 .84 RPM
SRP017611_kidney 0 .00 RPM 137 .68 RPM
SRP017611_liver 0 .00 RPM 37 .25 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_1050 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1050 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1050 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000035001 retrocopy
retro_amel_797,
Bos taurus ENSBTAG000000033421 retrocopy
retro_btau_1545,
Canis familiaris ENSCAFG000000039052 retrocopies
retro_cfam_1526, retro_cfam_2056,
Choloepus hoffmanni ENSCHOG000000091719 retrocopies
retro_chof_1327, retro_chof_2200, retro_chof_238, retro_chof_2691, retro_chof_332, retro_chof_425, retro_chof_628, retro_chof_74, retro_chof_968,
Callithrix jacchus ENSCJAG000000052576 retrocopies
retro_cjac_1600, retro_cjac_1738, retro_cjac_2452, retro_cjac_3020, retro_cjac_631, retro_cjac_850,
Dasypus novemcinctus ENSDNOG0000000686710 retrocopies
retro_dnov_1736, retro_dnov_1796, retro_dnov_185, retro_dnov_2436, retro_dnov_2653, retro_dnov_315, retro_dnov_357, retro_dnov_63, retro_dnov_752, retro_dnov_770,
Equus caballus ENSECAG000000111984 retrocopies
retro_ecab_1110, retro_ecab_173, retro_ecab_57, retro_ecab_681,
Felis catus ENSFCAG000000280331 retrocopy
retro_fcat_1175,
Homo sapiens ENSG000001235055 retrocopies
retro_hsap_3315, retro_hsap_3630, retro_hsap_3922, retro_hsap_4917, retro_hsap_547,
Gorilla gorilla ENSGGOG000000064665 retrocopies
retro_ggor_1304, retro_ggor_2448, retro_ggor_2640, retro_ggor_3070, retro_ggor_498,
Loxodonta africana ENSLAFG000000132032 retrocopies
retro_lafr_1040, retro_lafr_770,
Macropus eugenii ENSMEUG000000106301 retrocopy
retro_meug_1558,
Myotis lucifugus ENSMLUG000000056664 retrocopies
retro_mluc_1675, retro_mluc_1687, retro_mluc_2625, retro_mluc_538,
Macaca mulatta ENSMMUG000000005356 retrocopies
retro_mmul_1606, retro_mmul_1742, retro_mmul_1841, retro_mmul_2076, retro_mmul_2383, retro_mmul_2648,
Mus musculus ENSMUSG000000752321 retrocopy
retro_mmus_47,
Nomascus leucogenys ENSNLEG000000128184 retrocopies
retro_nleu_2758, retro_nleu_2983, retro_nleu_720, retro_nleu_812,
Otolemur garnettii ENSOGAG000000301507 retrocopies
retro_ogar_1108, retro_ogar_1152, retro_ogar_1608, retro_ogar_1962, retro_ogar_3163, retro_ogar_354, retro_ogar_366,
Pongo abelii ENSPPYG000000169244 retrocopies
retro_pabe_2977, retro_pabe_3194, retro_pabe_3826, retro_pabe_505,
Pan troglodytes ENSPTRG000000185015 retrocopies
retro_ptro_2157, retro_ptro_2453, retro_ptro_2667, retro_ptro_3280, retro_ptro_411,
Rattus norvegicus ENSRNOG00000000585 1 retrocopy
retro_rnor_1050 ,
Sorex araneus ENSSARG000000143873 retrocopies
retro_sara_274, retro_sara_614, retro_sara_760,
Sus scrofa ENSSSCG000000043921 retrocopy
retro_sscr_1042,
Ictidomys tridecemlineatus ENSSTOG000000002054 retrocopies
retro_itri_1402, retro_itri_1859, retro_itri_598, retro_itri_943,




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