RetrogeneDB ID: retro_ptro_1044

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:32119570..32120424(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM17
• Ensembl ID: ENSPTRG00000002265
• Aliases: None
• Description: None

Sequence

>retro_ptro_1044
AGAGAGGAAGGACAAAGACAGCGGGAGCTGGAAAGACAGAAGGAAATAGAAGAAAGAGAAGAAAGGCATAAATACAGACA
TGATGCACGTGAGTTTTCAAGGAGATCAGATCCGGATTCTGATGAAGATGAAGATTAGGAGCGAGAGAAGAGGAAAACAA
GTATGGGCGGAGCTGCTATTGCCTCACCCACTTCTCTGGCAGTAAAAGACAGTTGCCCCGAGATTTTCCTTATGAAGAGG
ACTCAAGACCTCGATCACAGTCTTCCAAAACTGCCATTCCTCCCCCAGTGTACGAGGAACAAGACAGACCGAGATCTCCA
ACCCGGCCCAGCGCAACTCCTTCCTCGCTAACTTGGGGGGCACGGTGGCGCACAAGATCATACAGAAGTACGGCTTCCGG
GAGGGCCAGGGTCTGGGGAAGCACGAGCAGGGGCTGAGCACCGCCTTTTCGGTGGAGAAGACCAGCAAGCTTGGTGGCAA
GATCATCGTGGGTGACGCCACGGAGAAAGATGCATCCAAGAAGTCAGATTCAAATCCACTGACTGAAATACTTAAGTGTC
CTAATAAAGTGGTCCTACTAAGGAACATGGTTGGTGCGGGAAAGGTGGATGAAGACTTGGAAGTTAAAACCAAGGAAGAA
CGTGAAAAATATCTCAAAGTTGGGAAAAGTGTGTTGTTTGAAATTCTGGTGCCCCGATGATGAAGCAGTACGGATATTTT
TAGAATTTGAGAGAGTTAAATCAGCAATTCAAGCGGTTATTGACTCGAATGGGAGGTATTTTGGTGGACAGGTGGCAAAT
GCATGTTTCTACAATTTGGAAAAATTCAGTGTCTTGGATTTGGCAGAACAAGTT

Alignment

ORF - retro_ptro_1044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.98 %
• Parental protein coverage: 71.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  REERQRQRELERQKEIEEREKRRKDRHEASGFARRPDPDSDEDEDYERERRKRSMGGAAIAPP-TSLVEK
          REE.QRQRELER...........K.RH.A..F.RR.DPDSDEDED.ERE.......G.A.....T.....
Retrocopy REEGQRQRELERXXXXXXXXXXHKYRHDAREFSRRSDPDSDEDED*ERE-KRKTSMGGAAIAS<THFSGS

Parental  DKELPRDFPYEEDSRPRSQSSKAAIPPPVYEEQDRPRSPT-GPS-NSFLANMGGTVAHKIMQKYGFREGQ
          ...LPRDFPYEEDSRPRSQSSK.AIPPPVYEEQDRPRSPT.GP..NSFLAN.GGTVAHKI.QKYGFREGQ
Retrocopy KRQLPRDFPYEEDSRPRSQSSKTAIPPPVYEEQDRPRSPT>GPA>NSFLANLGGTVAHKIIQKYGFREGQ

Parental  GLGKHEQGLSTALSVEKTSKRGGKIIVGDATEKDASKKSDSNPLTEILKCPTKVVLLRNMVGAGEVDEDL
          GLGKHEQGLSTA.SVEKTSK.GGKIIVGDATEKDASKKSDSNPLTEILKCP.KVVLLRNMVGAG.VDEDL
Retrocopy GLGKHEQGLSTAFSVEKTSKLGGKIIVGDATEKDASKKSDSNPLTEILKCPNKVVLLRNMVGAGKVDEDL

Parental  EVETKEECEKYGKVGKCVIFEI-PGAP-DDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLD
          EV.TKEE.EKY.KVGK.V.FEI..GAP.DDEAVRIFLEFERV.SAI.AV.D.NGRYFGG.V..ACFYNL.
Retrocopy EVKTKEEREKYLKVGKSVLFEI<SGAP<DDEAVRIFLEFERVKSAIQAVIDSNGRYFGGQVANACFYNLE

Parental  KFRVLDLAEQV
          KF.VLDLAEQV
Retrocopy KFSVLDLAEQV

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	0.04 RPM	39.16 RPM
SRP007412_cerebellum	0.22 RPM	61.01 RPM
SRP007412_heart	0.15 RPM	61.62 RPM
SRP007412_kidney	0.18 RPM	66.71 RPM
SRP007412_liver	0.00 RPM	52.60 RPM
SRP007412_testis	21.29 RPM	122.03 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1044 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1044 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1044 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1551
Pongo abelii	retro_pabe_1284

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021951	2 retrocopies	retro_btau_1057, retro_btau_530,
Canis familiaris	ENSCAFG00000005206	1 retrocopy	retro_cfam_844,
Callithrix jacchus	ENSCJAG00000020573	1 retrocopy	retro_cjac_432,
Equus caballus	ENSECAG00000008939	1 retrocopy	retro_ecab_547,
Erinaceus europaeus	ENSEEUG00000013077	1 retrocopy	retro_eeur_390,
Homo sapiens	ENSG00000134453	1 retrocopy	retro_hsap_1551,
Macropus eugenii	ENSMEUG00000011347	1 retrocopy	retro_meug_438,
Macaca mulatta	ENSMMUG00000015152	2 retrocopies	retro_mmul_1209, retro_mmul_771,
Mus musculus	ENSMUSG00000037197	1 retrocopy	retro_mmus_2855,
Otolemur garnettii	ENSOGAG00000015687	1 retrocopy	retro_ogar_1119,
Pongo abelii	ENSPPYG00000002067	1 retrocopy	retro_pabe_1284,
Pan troglodytes	ENSPTRG00000002265	1 retrocopy	retro_ptro_1044 ,
Ictidomys tridecemlineatus	ENSSTOG00000013591	1 retrocopy	retro_itri_1376,
Tursiops truncatus	ENSTTRG00000001344	1 retrocopy	retro_ttru_1758,