RetrogeneDB ID: retro_ptro_3213

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:48810083..48811025(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: OAT
• Ensembl ID: ENSPTRG00000003028
• Aliases: None
• Description: None

Sequence

>retro_ptro_3213
GTCCAAGGCCCTCCAACCTCTGACTACATTTTTGAAAGGGAATCTAAGTGTGGTGCGCACAATTACCATCCTTTACCTGT
AGCCCTGGAGAGAGGAAAATGTATTTTCTTATGGGATGTAGAAGGCAGAAAATATTTTGACTTTCTGAGTTCTTACAGTG
CTGTCAACCAAGGGCATTGTCACCCCAAGATTGTGAATGCACTAAAGAGTCAAGGGAAGAAATTGACCTTAACCTCTAGA
GCTTTCTATAATAACGTACTTGGTGAATATGAGGAGTATATTACTAAACTTTTCAACTACCACAAAGTTCTTCCTATGAA
TACAGGAATGGAAGCTGGAGAGACTGCCTGTAAACTAGCTCATAAGTGGGGCTATACTGTGAAGGGCATTCAGAAATACA
AAGCAAAGGTTATTTTCGCAGCTGGAAACTTTTGGGGTAGGACGTTTTCTGCTATCTCCAGTTCCACAGACCTGACGAGT
TATGATGGTTTTGGACCGTTTATGCCTGGCTTCGACGTCATTCCCTGCAATGATCTGCCTGCACTGGAGAGTGCTTTTCA
GAATCCAAATGTGGCTGCATTCATGGTAGAACCAATTCAGGGTGAAGCAGGTGTTGTTCCAGATCCAGGTTACTTAATGG
GAGTGTGAGAGCTCTGCACCAGGCACCAGGATCTGTATATTGCTGATGAAATACAGTCAGGATAGGCCAGAACTGGTAGA
TGGCTGGCTGTTGATCATGAAAATGTCAGACCTGATATAGTCCTCCTTGGAAAGGCCCTTTCTGGGGGCTGATACTCTGT
GTCTGCAGTGCTGTGGGACGATGACATAATGCTGACCATTAAGCCAGGGGAACGTGGGTCCACATACGGTGGCAATCCAC
TAGGCTGCCAAGTGACAATTGCAGCCCTTGAGGTTTTAGAAGAAGAAAACCTTGCTGAAAAT

Alignment

ORF - retro_ptro_3213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.16 %
• Parental protein coverage: 71.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQGPPTSDDIFEREYKYGAHNYHPLPVALERGKGIYLWDVEGRKYFDFLSSYSAVNQGHCHPKIVNALKS
          VQGPPTSD.IFERE.K.GAHNYHPLPVALERGK.I.LWDVEGRKYFDFLSSYSAVNQGHCHPKIVNALKS
Retrocopy VQGPPTSDYIFERESKCGAHNYHPLPVALERGKCIFLWDVEGRKYFDFLSSYSAVNQGHCHPKIVNALKS

Parental  QVDKLTLTSRAFYNNVLGEYEEYITKLFNYHKVLPMNTGVEAGETACKLARKWGYTVKGIQKYKAKIVFA
          Q..KLTLTSRAFYNNVLGEYEEYITKLFNYHKVLPMNTG.EAGETACKLA.KWGYTVKGIQKYKAK..FA
Retrocopy QGKKLTLTSRAFYNNVLGEYEEYITKLFNYHKVLPMNTGMEAGETACKLAHKWGYTVKGIQKYKAKVIFA

Parental  AGNFWGRTLSAISSSTDPTSYDGFGPFMPGFDIIPYNDLPALERALQDPNVAAFMVEPIQGEAGVVVPDP
          AGNFWGRT.SAISSSTD.TSYDGFGPFMPGFD.IP.NDLPALE.A.Q.PNVAAFMVEPIQGEAG.VVPDP
Retrocopy AGNFWGRTFSAISSSTDLTSYDGFGPFMPGFDVIPCNDLPALESAFQNPNVAAFMVEPIQGEAG-VVPDP

Parental  GYLMGVRELCTRHQVLFIADEIQTGLARTGRWLAVDYENVRPDIVLLGKALSGGLYPVSAVLCDDDIMLT
          GYLMGV.ELCTRHQ.L.IADEIQ.G.ARTGRWLAVD.ENVRPDIVLLGKALSGG.Y.VSAVL.DDDIMLT
Retrocopy GYLMGV*ELCTRHQDLYIADEIQSG*ARTGRWLAVDHENVRPDIVLLGKALSGG*YSVSAVLWDDDIMLT

Parental  IKPGEHGSTYGGNPLGCRVAIAALEVLEEENLAEN
          IKPGE.GSTYGGNPLGC.V.IAALEVLEEENLAEN
Retrocopy IKPGERGSTYGGNPLGCQVTIAALEVLEEENLAEN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	92.77 RPM
SRP007412_cerebellum	0.11 RPM	68.69 RPM
SRP007412_heart	0.03 RPM	20.49 RPM
SRP007412_kidney	0.00 RPM	80.65 RPM
SRP007412_liver	0.00 RPM	33.88 RPM
SRP007412_testis	0.00 RPM	28.24 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3213 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3213 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3213 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3754

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012633	1 retrocopy	retro_cjac_2462,
Homo sapiens	ENSG00000065154	1 retrocopy	retro_hsap_4828,
Gorilla gorilla	ENSGGOG00000000848	1 retrocopy	retro_ggor_3010,
Macropus eugenii	ENSMEUG00000005655	1 retrocopy	retro_meug_613,
Mus musculus	ENSMUSG00000030934	1 retrocopy	retro_mmus_3475,
Nomascus leucogenys	ENSNLEG00000000482	2 retrocopies	retro_nleu_2176, retro_nleu_503,
Pongo abelii	ENSPPYG00000002737	2 retrocopies	retro_pabe_2989, retro_pabe_3754,
Pan troglodytes	ENSPTRG00000003028	1 retrocopy	retro_ptro_3213 ,
Sus scrofa	ENSSSCG00000010734	1 retrocopy	retro_sscr_1181,
Tursiops truncatus	ENSTTRG00000004225	1 retrocopy	retro_ttru_87,