RetrogeneDB ID:

retro_rnor_1663

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:2:185687430..185688541(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000028120
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Psat1
Ensembl ID:ENSRNOG00000013971
Aliases:Psat1, Psa1
Description:phosphoserine aminotransferase [Source:RefSeq peptide;Acc:NP_942033]


Retrocopy-Parental alignment summary:






>retro_rnor_1663
ATGGAAGCCACCAAGCAAGTGATTAACTTTGGGCCCGGGCCTGCCAAGTTACGATACTCGGTTTTGTTAGAGATACAGAA
GCTGCTACTAGACTACAAAGGCCTTGGCATCAACGTGCTTGAAATGAGTCACAGGTCATCAGATTTCGCCAAGATTATTA
GCAACACAGAGAATCTTGTGAGGGAATTGCTAGCTGTTCCCAACAACTACAAGGTGATCTTTGTACAAGGAGGTGGGACT
GGCCAGTTCAGTGCCGTCCCTTTAAATCTTACTGGCCTGAAAGCTGGAAGGTGTGCCCACTATGTGGTGACCGGAGCTTG
GTCAGCTAAGGCTGCGGAAGAAGCCAAGAAGTTTGGGACTGTGAACATTGTTCATCCTAAACTTGGAAATTACACAAAAA
TTCCAGACCCAAGCACCTGGAACCTCAACCCAGACACCTCCTATGTGTACCTCTGTGCAAACGAGACTGTGCATGGCGTG
GAGTTTGACTTCATACCTGACATCAAGGGAGCAGTGCTGGTCTGTGACATGTCTTCAAACTTCTTATCCAGGCCAGTGGA
CGTTTCCAAGTTTGGTGTGATTTTCGCTGGTGCTCAGAAGAATGTTGGCTCTGCTGGGGTGACGGTGGTAATTGTCTGTG
ATGACCTGCTGGGGTTCGCCCTCAGAGAGTGCCCATCAGTCCTTGACTACAAAGTGCAGGCTGGGAACAACTCTTGTTAT
AACACACCTCCATGCTTCAGCATCTACGTCATGGGCATGGTCCTGGAATGGATCGAGAACAATGGTGGGGCCGCAGCCAT
GGAGAAGCTCAGCTCCGTCAAATCCCAAATGATTTATGAGATTATTGATAATTCTCAAGGATTTTATGTTGTGTCCGGTG
GAGCGCCAGAATAGAAGCAGGATGAACATTCCGTTTCGCATTGGCAAAGGCAAAGGGAATGAAGCTCTGGAGAAGCGGTT
TCTTGATAAGGCCGTAGAACTCAACATGATCTCCTTGAAGCGGCACAGGTCGGTGGGAGGCATCCGAGCCTCTCTGTATA
ATGCTGTCACCACCGAAGATGTTGAGAAGTTGGCTGCCTTCATGAAGAACTTTTTGGAGATGCATCAGCTG

ORF - retro_rnor_1663 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.99 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMEATKQVVNFGPGPAKLPYSVLLEIQKQLLDYKGLGISVLEMSHRSPDFAKIISNTENLVRELLAVPNNY
MEATKQV.NFGPGPAKL.YSVLLEIQK.LLDYKGLGI.VLEMSHRS.DFAKIISNTENLVRELLAVPNNY
RetrocopyMEATKQVINFGPGPAKLRYSVLLEIQKLLLDYKGLGINVLEMSHRSSDFAKIISNTENLVRELLAVPNNY
ParentalKVIFVQGGGTGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTVNIVHPKLGSYTKIPDPSTW
KVIFVQGGGTGQFSAVPLNL.GLKAGRCA.YVVTGAWSAKAAEEAKKFGTVNIVHPKLG.YTKIPDPSTW
RetrocopyKVIFVQGGGTGQFSAVPLNLTGLKAGRCAHYVVTGAWSAKAAEEAKKFGTVNIVHPKLGNYTKIPDPSTW
ParentalNLNPDASYVYFCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSRPVDVSKFGVIFAGAQKNVGSAGVTVV
NLNPD.SYVY.CANETVHGVEFDFIPD.KGAVLVCDMSSNFLSRPVDVSKFGVIFAGAQKNVGSAGVTVV
RetrocopyNLNPDTSYVYLCANETVHGVEFDFIPDIKGAVLVCDMSSNFLSRPVDVSKFGVIFAGAQKNVGSAGVTVV
ParentalIVRDDLLGFALRECPSVLDYKVQAGNNSLYNTPPCFSIYVMDMVLEWIKNNGGAAAMEKLSSVKSQMIYE
IV.DDLLGFALRECPSVLDYKVQAGNNS.YNTPPCFSIYVM.MVLEWI.NNGGAAAMEKLSSVKSQMIYE
RetrocopyIVCDDLLGFALRECPSVLDYKVQAGNNSCYNTPPCFSIYVMGMVLEWIENNGGAAAMEKLSSVKSQMIYE
ParentalIIDNSQGFYV-CPVERQNRSRMNIPFRIGNSKGDEALEKRFLDKAVELNMISLKGHRSVGGIRASLYNAV
IIDNSQGFYV.CPVERQNRSRMNIPFRIG..KG.EALEKRFLDKAVELNMISLK.HRSVGGIRASLYNAV
RetrocopyIIDNSQGFYV>CPVERQNRSRMNIPFRIGKGKGNEALEKRFLDKAVELNMISLKRHRSVGGIRASLYNAV
ParentalTTEDVEKLAAFLRSFLVVHVL
TTEDVEKLAAF...FL..H.L
RetrocopyTTEDVEKLAAFMKNFLEMHQL

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 1 .08 RPM 71 .68 RPM
SRP017611_kidney 1 .12 RPM 134 .26 RPM
SRP017611_liver 0 .00 RPM 3 .23 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_1663 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1663 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1663 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068981 retrocopy
retro_amel_375,
Bos taurus ENSBTAG000000139601 retrocopy
retro_btau_1658,
Canis familiaris ENSCAFG000000015701 retrocopy
retro_cfam_269,
Choloepus hoffmanni ENSCHOG000000038171 retrocopy
retro_chof_2702,
Callithrix jacchus ENSCJAG000000033191 retrocopy
retro_cjac_1203,
Echinops telfairi ENSETEG000000041581 retrocopy
retro_etel_99,
Homo sapiens ENSG000001350693 retrocopies
retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Gorilla gorilla ENSGGOG000000154801 retrocopy
retro_ggor_407,
Loxodonta africana ENSLAFG000000179172 retrocopies
retro_lafr_1249, retro_lafr_660,
Macaca mulatta ENSMMUG000000118682 retrocopies
retro_mmul_1029, retro_mmul_2341,
Mustela putorius furoENSMPUG000000125661 retrocopy
retro_mputfur_808,
Nomascus leucogenys ENSNLEG000000029893 retrocopies
retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus ENSOCUG000000077651 retrocopy
retro_ocun_1092,
Pongo abelii ENSPPYG000000193133 retrocopies
retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes ENSPTRG000000210452 retrocopies
retro_ptro_1606, retro_ptro_316,
Rattus norvegicus ENSRNOG00000013971 1 retrocopy
retro_rnor_1663 ,
Tupaia belangeri ENSTBEG000000129461 retrocopy
retro_tbel_1577,
Tarsius syrichta ENSTSYG000000000932 retrocopies
retro_tsyr_1073, retro_tsyr_1212,


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