RetrogeneDB ID: retro_pabe_1284

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:31479382..31480031(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM17
• Ensembl ID: ENSPPYG00000002067
• Aliases: None
• Description: RNA binding motif protein 17 [Source:HGNC Symbol;Acc:16944]

Sequence

>retro_pabe_1284
GAAACCAGTGACTCAAAAACAGAAGGCTGGTCCAAAAACTTCAAACTTCTACAGTCTCGGCTTCAGGTGAAGAAGGCAGC
TCTCACTCAGGCAGAGAGCCAAAGGACGAAACAAGGTACAGTTCTTGCCCCAGTCATTGACCTAAAACGAGGTGGCTCCT
CAGATGACCGGGCAAATTGTGGACACACCACCGCATGTGCCAGCTGGGCTGAAGGATCCTGTTCCCAGTGGGTTTTCTGC
AGGGGAAGTTCTGATTCCCTTAGCTGACGAATATGATCCTATGTTTCCTAACGATTATGAGAAAGTAGTGAAACGCCAGA
GAGGAACGACAAAAACAGCGGGAGCTGGAAAGACAAAAGGAAATAGAAGAAAGAGAAAAAAGGCATAAATACAGACATGA
TGCACGTGAGTTTTCAAGTAGATCAGATCCGGATTCTGATGAAGATGAAGATTAGGAGCGAGAGAAGAGGAAAACAAGTA
TGGGTGGAACTGCCATTGCCCCACCCACTTCTCTGGCAGTAAAAGACAGTTACCCCGAGATTTTCCTTATGAAGAGGACT
CAAGACCTCGATCACAGTCTTCCAAAACTGCCATTCCTCCCCCAGTTTACGAGGAACAAGACAGACCGAGATCTCCAACC
CGGCCCAGC

Alignment

ORF - retro_pabe_1284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.07 %
• Parental protein coverage: 54.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ETSDSKTEGWSKNFKLLQSQLQVKKAALTQAKSQRTKQSTVLAPVIDLKRGGSSDDR-QIVDTPPHVAAG
          ETSDSKTEGWSKNFKLLQS.LQVKKAALTQA.SQRTKQ.TVLAPVIDLKRGGSSDDR.QIVDTPPHV.AG
Retrocopy ETSDSKTEGWSKNFKLLQSRLQVKKAALTQAESQRTKQGTVLAPVIDLKRGGSSDDR>QIVDTPPHVPAG

Parental  LKDPVPSGFSAGEVLIPLADEYDPMFPNDYEKVVKRQR-EERQRQRELERQKEIEEREKRRKDRHEASGF
          LKDPVPSGFSAGEVLIPLADEYDPMFPNDYEKVVKRQR.E.....RELERQKEIEEREKR.K.RH.A..F
Retrocopy LKDPVPSGFSAGEVLIPLADEYDPMFPNDYEKVVKRQR>ERQKQ-RELERQKEIEEREKRHKYRHDAREF

Parental  ARRPDPDSDEDEDYERERRKRSMGGAAIAPPTSLVEKDKELPRDF-PYEEDSRPRSQSSKAAIPPPVYEE
          ..R.DPDSDEDED.ERE.RK.SMGG.AIAPPTSL..KD...P..F.PYEEDSRPRSQSSK.AIPPPVYEE
Retrocopy SSRSDPDSDEDED*EREKRKTSMGGTAIAPPTSLAVKD-SYPEIF<PYEEDSRPRSQSSKTAIPPPVYEE

Parental  QDRPRSPTGPS
          QDRPRSPT.PS
Retrocopy QDRPRSPTRPS

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	0.06 RPM	42.79 RPM
SRP007412_cerebellum	0.36 RPM	50.34 RPM
SRP007412_heart	0.00 RPM	27.73 RPM
SRP007412_kidney	0.20 RPM	41.33 RPM
SRP007412_liver	0.06 RPM	31.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1284 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1284 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1284 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1551
Pan troglodytes	retro_ptro_1044

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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,