RetrogeneDB ID: retro_ptro_439

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:73243665..73244839(+)
• Located in intron of: ENSPTRG00000002649

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3D
• Ensembl ID: ENSPTRG00000020056
• Aliases: None
• Description: None

Sequence

>retro_ptro_439
ATGTCGGAAGGAAATGCAGTGAGCGAACCCAGCACTCTGCAAGGGCCCCGACCCCTCCTGACTGGGGCCCAGGAGCTCAG
CAGGCAGCGACTGGCACCCCTTCACCCCGGGCCGCCTTCCTTTCATCCGCTCTGGGAACCTTACCCTGGGGGTTGAGGTT
GGGGGTCAAGAAGAAAACCTTCACCCCAAATATCATCAGTCAGAAGAACCCAAGGAAGAAGTAACCGTCAAGAAGGAGAA
ACATGAAAGGGACAGAGATGGACAGAGAGAGGTGCATGAACAGGGATGAGGCCACCCAGAAGTGATCCAGTCCCACTCCA
TCTTTGAGAAGGTCCCAGCTGAAATGATGAAGAAAAAAGGAACTGGAATAAGAAAGTGAATGTGTCAGACATGAGACCTT
CTCATATCGTCCACATCAAAAAAGAGAAGAAAGAGTTGGACGAAGACACGAAACATCTCACCATGCTGTAGAAGGACGAT
TTCATCGATGACCCTGGGCTGAGGAATGACACTCGCAACATGCCTGTGCAGCTGCCACTGGCTCACTCAGGGCGGCTTTT
TAAGGAAGAAAACGATGAACCAGATGTTAAACCTTGGCTGGCTGGCCCCAAGAAAGAGGTGGGTGTACCTACTGTGAAAC
TGAAAGAGGAGCTACAAGATGAGGAGGAGGCCAAGATAAAGGCTCCTTCCAGAGCAGCCAGGAAGACCCCCGGGCCTCCC
GAAGGACATATCCGTGGCAGAGCTGCCCAGGGAGCTGAGCCTCACCAAGGAGGAGGAATTGCTGTTCCTCCAGTTGCCAG
ACACCCTCCCTGGCCACCCACCTATCCAGGACATCAAGCCCATCAAGGCAGAGGTACAGGGCAAGGACAGAGAGGTGGTA
CTCATCAAGCAGGAGAACGACCAGGAAGCCAGGCTGGCAAAGAATGCTTCTACCCTAGCTGACCTGACAGAGGGTCAGGT
TGGCAAGCTGCCCATCTGCAAGTCCGAACGGGTGCAACTCCTCCTGGGCAAGGTGACTCTGGACGTGACCATGGGAACCG
CCTGCTCTTTCCTGCAGGAGCTGGTGTCTGTGGGCCTTGGAGAGAGTAGGACTGGGGAGATGATAGACCTGGGACATGTG
AAGCACAAACTTCTGTGTTCCCCCGATTTTGAATCCCTCTTGGATCACAAACAC

Alignment

ORF - retro_ptro_439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.06 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSEGNAAGEPSTPGGPRPLLTGARGLIGRRPAPPLTP-GRLPSIRSRDLTLGGVKKKTFTPNIISRKIKE
          MSEGNA..EPST..GPRPLLTGA..L...R.A.PL.P.GRLP.IRS..LTL.GV.......N........
Retrocopy MSEGNAVSEPSTLQGPRPLLTGAQELSRQRLA-PLHP>GRLPFIRSGNLTL-GVEVGGQEENLHPKYHQS

Parental  EPKEEVTVKK-EKRERDRDRQREGHGRGRGRPEVIQSHSIFEQGPAEMMKKKG-NWDKTVDVSDMGPSHI
          E...E....K.EK.ERDRD.QRE.H..G.G.PEVIQSHSIFE..PAEMMKKKG.NW.K.V.VSDM.PSHI
Retrocopy EEPKEEVTVKKEKHERDRDGQREVHEQG*GHPEVIQSHSIFEKVPAEMMKKKG<NWNKKVNVSDMRPSHI

Parental  INIKKEKRETDEETKQILRMLEKDDFLDDPGLRNDTRNMPVQLPLAHSGWLFKEENDEPDVKPWLAGPKE
          ..IKKEK.E.DE.TK..L.ML.KDDF.DDPGLRNDTRNMPVQLPLAHSG.LFKEENDEPDVKPWLAGPK.
Retrocopy VHIKKEKKELDEDTKH-LTML*KDDFIDDPGLRNDTRNMPVQLPLAHSGRLFKEENDEPDVKPWLAGPKK

Parental  EDMEVDIPAVKVKEEPRDEEEEAKMKAPPKAARKT-PGLPKDVSVAELLRELSLTKEEELLFLQLPDTLP
          E...V..P.VK.KEE..D.EEEAK.KAP..AARKT.PGLPKD.SVAEL.RELSLTKEEELLFLQLPDTLP
Retrocopy E---VGVPTVKLKEELQD-EEEAKIKAPSRAARKT>PGLPKDISVAELPRELSLTKEEELLFLQLPDTLP

Parental  GQPPTQDIKPIKTEVQGEDGQVVLIKQEKDREAKLAENACTLADLTEGQVGKLLIRKSGRVQLLLGKVTL
          G.PP.QDIKPIK.EVQG.D..VVLIKQE.D.EA.LA.NA.TLADLTEGQVGKL.I.KS.RVQLLLGKVTL
Retrocopy GHPPIQDIKPIKAEVQGKDREVVLIKQENDQEARLAKNASTLADLTEGQVGKLPICKSERVQLLLGKVTL

Parental  DVTMGTACSFLQELVSVGLGDSRTGEMTVLGHVKHKLVCSPDFESLLDHKH
          DVTMGTACSFLQELVSVGLG.SRTGEM..LGHVKHKL.CSPDFESLLDHKH
Retrocopy DVTMGTACSFLQELVSVGLGESRTGEMIDLGHVKHKLLCSPDFESLLDHKH

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	0.05 RPM	12.51 RPM
SRP007412_cerebellum	0.00 RPM	15.16 RPM
SRP007412_heart	0.06 RPM	9.62 RPM
SRP007412_kidney	0.05 RPM	15.22 RPM
SRP007412_liver	0.20 RPM	16.30 RPM
SRP007412_testis	0.00 RPM	47.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_439 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_439 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_596
Pongo abelii	retro_pabe_594
Macaca mulatta	retro_mmul_2449

---

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,