RetrogeneDB ID:

retro_hsap_4828

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:48305880..48306831(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226971
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:OAT
Ensembl ID:ENSG00000065154
Aliases:OAT, GACR, HOGA, OATASE, OKT
Description:ornithine aminotransferase [Source:HGNC Symbol;Acc:8091]


Retrocopy-Parental alignment summary:






>retro_hsap_4828
AAGAAAACAGTCCAAGGCCCTCCAACCTCTGACTACATTTTTGAAAGGGAATCTAAGTGTGGTGCGCACAATTACCATCC
TTTACCTGTAGCCCTGGAGAGAGGAAAATGTATTTACTTATGGGATGTAGAAGGCAGAAAATATTTTGACTTTCTGAGTT
CTTACAGTGCTGTCAACCAAGGGCATTGTCACCCCAAGATTGTGAATGCACTAAAGAGTCAAGGGAAGAAATTGACCTTA
ACCTCTAGAGCTTTCTATAATAACGTACTTGGTGAATATGAGGAGTATATTACTAAACTTTTCAACTACCACAAAGTTCT
TCCTATGAATACAGGAATGGAAGCTGGAGAGACTGCCTGTAAACTAGCTCATAAGTGGGGCTATACTGTGAAGGGCATTC
AGAAATACAAAGCAAAGGTTATTTCCGCAGCTGGAAACTTTTGGGGTAGGACGTTTTCTGCTATCTCCAGTTCCACAGAC
CTGACGAGTTATGATGGTTTTGGACCGTTTATGCCTGGCTTCGACGTCATTCCCTGCAATGATCTGCCTGCACTGGAGAG
TGCTTTTCAGAATCCAAATGTGGCTGCATTCATGGTAGAACCAATTCAGGGTGAAGCAGGTGTTGTTCCAGATCCAGGTT
ACTTAATGGGAGTGCGAGAGCTCTGCACCAGGCACCAGGATCTGTATATTGCTGATGAAATACAGTCAGGATAGGCCAGA
ACTGGTAGATGGCTGGCTGTTGATCATGAAAATGTCAGACCTGATATAGTCCTCCTTGGAAAGGCCCTTTCTGGGGGCTG
ATACTCTGTGTCTGCAGTGCTGTGGGACGATGACATAATGCTGACCATTAAGCCAGGGGAATGTGGGTCCACATACGGTG
GCAATCCACTAGGCTGCCAAGTGACAATTGCAGCCCTTGAGGTTTTAGAAGAAGAAAACCTTGCTGAAAAT

ORF - retro_hsap_4828 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.57 %
Parental protein coverage: 72.44 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKKTVQGPPTSDDIFEREYKYGAHNYHPLPVALERGKGIYLWDVEGRKYFDFLSSYSAVNQGHCHPKIVNA
KKTVQGPPTSD.IFERE.K.GAHNYHPLPVALERGK.IYLWDVEGRKYFDFLSSYSAVNQGHCHPKIVNA
RetrocopyKKTVQGPPTSDYIFERESKCGAHNYHPLPVALERGKCIYLWDVEGRKYFDFLSSYSAVNQGHCHPKIVNA
ParentalLKSQVDKLTLTSRAFYNNVLGEYEEYITKLFNYHKVLPMNTGVEAGETACKLARKWGYTVKGIQKYKAKI
LKSQ..KLTLTSRAFYNNVLGEYEEYITKLFNYHKVLPMNTG.EAGETACKLA.KWGYTVKGIQKYKAK.
RetrocopyLKSQGKKLTLTSRAFYNNVLGEYEEYITKLFNYHKVLPMNTGMEAGETACKLAHKWGYTVKGIQKYKAKV
ParentalVFAAGNFWGRTLSAISSSTDPTSYDGFGPFMPGFDIIPYNDLPALERALQDPNVAAFMVEPIQGEAGVVV
..AAGNFWGRT.SAISSSTD.TSYDGFGPFMPGFD.IP.NDLPALE.A.Q.PNVAAFMVEPIQGEAG.VV
RetrocopyISAAGNFWGRTFSAISSSTDLTSYDGFGPFMPGFDVIPCNDLPALESAFQNPNVAAFMVEPIQGEAG-VV
ParentalPDPGYLMGVRELCTRHQVLFIADEIQTGLARTGRWLAVDYENVRPDIVLLGKALSGGLYPVSAVLCDDDI
PDPGYLMGVRELCTRHQ.L.IADEIQ.G.ARTGRWLAVD.ENVRPDIVLLGKALSGG.Y.VSAVL.DDDI
RetrocopyPDPGYLMGVRELCTRHQDLYIADEIQSG*ARTGRWLAVDHENVRPDIVLLGKALSGG*YSVSAVLWDDDI
ParentalMLTIKPGEHGSTYGGNPLGCRVAIAALEVLEEENLAEN
MLTIKPGE.GSTYGGNPLGC.V.IAALEVLEEENLAEN
RetrocopyMLTIKPGECGSTYGGNPLGCQVTIAALEVLEEENLAEN

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
bodymap2_adipose 0 .00 RPM 56 .75 RPM
bodymap2_adrenal 0 .00 RPM 67 .51 RPM
bodymap2_brain 0 .07 RPM 141 .20 RPM
bodymap2_breast 0 .00 RPM 93 .39 RPM
bodymap2_colon 0 .00 RPM 106 .12 RPM
bodymap2_heart 0 .00 RPM 33 .65 RPM
bodymap2_kidney 0 .00 RPM 82 .47 RPM
bodymap2_liver 0 .00 RPM 95 .01 RPM
bodymap2_lung 0 .02 RPM 89 .38 RPM
bodymap2_lymph_node 0 .16 RPM 74 .36 RPM
bodymap2_ovary 0 .00 RPM 100 .91 RPM
bodymap2_prostate 0 .00 RPM 98 .79 RPM
bodymap2_skeletal_muscle 0 .00 RPM 24 .74 RPM
bodymap2_testis 0 .00 RPM 101 .17 RPM
bodymap2_thyroid 0 .00 RPM 88 .56 RPM
bodymap2_white_blood_cells 0 .00 RPM 55 .72 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4828 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4828 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4828 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4828 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4828 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_3010
Parental genes homology:
Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000126331 retrocopy
retro_cjac_2462,
Homo sapiens ENSG00000065154 1 retrocopy
retro_hsap_4828 ,
Gorilla gorilla ENSGGOG000000008481 retrocopy
retro_ggor_3010,
Macropus eugenii ENSMEUG000000056551 retrocopy
retro_meug_613,
Mus musculus ENSMUSG000000309341 retrocopy
retro_mmus_3475,
Nomascus leucogenys ENSNLEG000000004822 retrocopies
retro_nleu_2176, retro_nleu_503,
Pongo abelii ENSPPYG000000027372 retrocopies
retro_pabe_2989, retro_pabe_3754,
Pan troglodytes ENSPTRG000000030281 retrocopy
retro_ptro_3213,
Sus scrofa ENSSSCG000000107341 retrocopy
retro_sscr_1181,
Tursiops truncatus ENSTTRG000000042251 retrocopy
retro_ttru_87,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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