RetrogeneDB ID: retro_pabe_594

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:60519677..60520652(-)
• Located in intron of: ENSPPYG00000002319

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3D
• Ensembl ID: ENSPPYG00000018419
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide D, 44kDa [Source:HGNC Symbol;Acc:1080]

Sequence

>retro_pabe_594
GAAGAACCCAAGGAAGAAGTAACCGTCAAGAAGGAGAAACATGAAAGGGACAGAGATGGACACAGAGAGGTGCATAGACA
GGGATGAGGCCACCCAGAAGTGATCCAGTCCCACTCCATCTTTGAGAAGGGCCCAGCTGAAATGATGAAGAAAAATGGAA
CTGGAATAAGAAAGTGAATGTGTCAGACATGGGACCTTCTCATATTGTCAACATCAAAAAAGAGAAGAAAGAGTTGGACG
AAGACATGAAACATCTCACCATGCTGGAGAAGGACAATTTCATCGATGACCCTGGGCTGAGGAATGACACTCGAAACATG
CCTGTGCAGCTGCCACTGGCTCACTCAGGGTGGCTTTTTAAGGAAGAAAATGATGAACCAGATGTTAAATCTTGGCTGGC
TGGCCCCAAGGAAGAGGTGGGTGTACCTACTGTGAAACTGAAAGAGGAGCTACAAGATGAGGAGGAGGAGGCCAAGATGC
AGGCTCCTTCCAGAGCAGCCAGGAAGACCCCTGGGCCTCCTGAAGGACATACCCGTGGCAGAGCTGCCCAGGGAGCTGAG
CCTCACCAAGGAGGAGGAATTGCTGTTCCTCCAGTTGCCAGACAGCCTCACTGGCCACCCACCTATCCAGGACATCAAGC
CTATCAAGGCAGAGGTACGGGGCAAGGACGGACAGGTGGTACTCATCAAGCAGGATAACGACCAGGAAGCCAGGCTGGCA
GAGAATGCTTCTACCCTAGCTGACCTGACAGAGGGTCAGGTTGGCAAGCTGCCCATCTGCAAGTCCGAAAGGGTGCAACT
CCTCCTGGGCAAGGTGACTCTGGACGTGACCATGGGAACGGCCTGCTCTTTCCTGAAGGAGCTGGTGTCTGTGGGCCTTG
GAGAGAGTAGGACTGGGGAGATGATAGACCTGGGACATGTGAAGCACAAACTTCTGTGTTCTCCCGATTTTGAATCCCTC
TTGGATCACAAACAC

Alignment

ORF - retro_pabe_594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.27 %
• Parental protein coverage: 82.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEPKEEVTVKKEKRERDRDRQREGHGRGRGRPEVIQSHSIFEQGPAEMMKKKG-NWDKTVDVSDMGPSHI
          EEPKEEVTVKKEK.ERDRD..RE.H..G.G.PEVIQSHSIFE.GPAEMMKK.G.NW.K.V.VSDMGPSHI
Retrocopy EEPKEEVTVKKEKHERDRDGHREVHRQG*GHPEVIQSHSIFEKGPAEMMKKNG<NWNKKVNVSDMGPSHI

Parental  INIKKEKRETDEETKQILRMLEKDDFLDDPGLRNDTRNMPVQLPLAHSGWLFKEENDEPDVKPWLPGPKE
          .NIKKEK.E.DE..K..L.MLEKD.F.DDPGLRNDTRNMPVQLPLAHSGWLFKEENDEPDVK.WL.GPKE
Retrocopy VNIKKEKKELDEDMKH-LTMLEKDNFIDDPGLRNDTRNMPVQLPLAHSGWLFKEENDEPDVKSWLAGPKE

Parental  EDMEVDIPAVKVKEEPRDEEEEAKMKAPPRAARKTPGLP-KDVSVAELLRELSLTKEEELLFLQLPDTLP
          ...EV..P.VK.KEE..DEEEEAKM.AP.RAARKTPG.P.KD..VAEL.RELSLTKEEELLFLQLPD.L.
Retrocopy ---EVGVPTVKLKEELQDEEEEAKMQAPSRAARKTPGPP>KDIPVAELPRELSLTKEEELLFLQLPDSLT

Parental  GQPPTQDIKPIKTEVQGEDGQVVLIKQEKDREAKLAENACTLADLTEGQVGKLLIRKSGRVQLLLGKVTL
          G.PP.QDIKPIK.EV.G.DGQVVLIKQ..D.EA.LAENA.TLADLTEGQVGKL.I.KS.RVQLLLGKVTL
Retrocopy GHPPIQDIKPIKAEVRGKDGQVVLIKQDNDQEARLAENASTLADLTEGQVGKLPICKSERVQLLLGKVTL

Parental  DVTMGTACSFLQELVSVGLGDSRTGEMTVLGHVKHKLVCSPDFESLLDHKH
          DVTMGTACSFL.ELVSVGLG.SRTGEM..LGHVKHKL.CSPDFESLLDHKH
Retrocopy DVTMGTACSFLKELVSVGLGESRTGEMIDLGHVKHKLLCSPDFESLLDHKH

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	10.23 RPM
SRP007412_cerebellum	0.12 RPM	6.08 RPM
SRP007412_heart	0.03 RPM	8.04 RPM
SRP007412_kidney	0.03 RPM	10.18 RPM
SRP007412_liver	0.06 RPM	6.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_594 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_594 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_596
Pan troglodytes	retro_ptro_439
Macaca mulatta	retro_mmul_2449

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013488	1 retrocopy	retro_dnov_1681,
Equus caballus	ENSECAG00000025090	1 retrocopy	retro_ecab_43,
Erinaceus europaeus	ENSEEUG00000007632	2 retrocopies	retro_eeur_277, retro_eeur_705,
Homo sapiens	ENSG00000168495	1 retrocopy	retro_hsap_596,
Macropus eugenii	ENSMEUG00000000465	1 retrocopy	retro_meug_1550,
Myotis lucifugus	ENSMLUG00000002109	1 retrocopy	retro_mluc_2339,
Macaca mulatta	ENSMMUG00000023226	1 retrocopy	retro_mmul_2449,
Monodelphis domestica	ENSMODG00000009491	1 retrocopy	retro_mdom_988,
Nomascus leucogenys	ENSNLEG00000015502	1 retrocopy	retro_nleu_2218,
Pongo abelii	ENSPPYG00000018419	1 retrocopy	retro_pabe_594 ,
Pan troglodytes	ENSPTRG00000020056	1 retrocopy	retro_ptro_439,
Tursiops truncatus	ENSTTRG00000012745	1 retrocopy	retro_ttru_1189,