RetrogeneDB ID: retro_ecab_547

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:19100391..19101594(-)
• Located in intron of: ENSECAG00000024919

Retrocopy information

• Ensembl ID: ENSECAG00000001379
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBM17
• Ensembl ID: ENSECAG00000008939
• Aliases: None
• Description: RNA binding motif protein 17 [Source:HGNC Symbol;Acc:16944]

Sequence

>retro_ecab_547
ATGTCCCTGTATGACGACCTGGGAGTGGAGACCAGTGACTCGAAAACAGAAGGCTGGTCCAAAAACTTCACACTTCTGCA
GTCTCAGCTTCAGGTGAAGAGGGCAGCTCTCACTCAGGCAAAGAGCCAGAGGACAAAACAAAGTACAGTCCTCGCCCCAG
TCATCGACCTAAAGCGAGGTGGCTCTTCAGACGACCGGCAGATCGTGGACACCCCGCCGCACGTAGCCGCCGGCCTGAAG
GATCCTGTTCCCAGTGGATTTTCTGCAGGAGAAGTTCTGATTCCTTTAGCTGATGAATATGATCCTAGGTTTCCTAATGA
TTATGAGAAAGTAGTGAAGCGCCAAAGAGAAGAACGACAGAGACAGCGGGAGCTGGAAAGACAAAAAGAAATAGAAGAGA
GAGAAAAGAGGCGTAAAGACAGACATGAAGCTAGTGGGTTTTCAAGGCGAACAGATCCAGATTCTGATGAAGATGAAGAT
TATGAGCGAGAGAGGAGGAAAAGAAGTATGGGCGGAGCTGCCATCACACCACCCACTTCTCTTGTAGAGAAAGACAAAGA
GTTACCCCGAGATTTTCCACATGAAGAGGATTCAAGACCTCGCTCACAGTCTTCCAAAGCTGGTATCCCTCCCCCGGTGT
ACGAGGAGCAAGACAAACCCCGATCTCCGACCGGACCTGGCAACTCCTTCCTTGCCAACATGGGTGGCACAGTAGCACAT
AAAATCATGCAGAAGTATGGCTTCCGGGAAGGCCAGGGTCTTGGGAAGCACGAGCAAGGGCTGAGCATGGCGTTGTCAGT
GGAGAAGACAAGCAAGCGAGGCGGCAAGATCATTGTGGGCGACGCCACGGAGAAAGATGCAGCCAAGAAGTCGGATTCAA
ATCCACTGACTGAAATACTGAAGTGTCCTACTAAAGTGGTCCTACTAAGGAACATGGTTGGTGCAGGAGAGGTAGATGAA
GACTTGGAAGTTGAAACCAAGGAAGAATGTGAAAAATATGGCAAAGTTGGAAAATGTGTGATATTTGAAATTCTTGGTGC
CCCTGATGATGAAGCAGTACGAATATTTTTAGAATTTGAAAGAGTTGAATCAGCAATTAAAGCTGTTGTTGATCTGAACG
GGAGGTATTTTGGTGGACGGGTGGTAAAAGCATGTTTCTACAATTTGGATAAATTCAGGGTCTTGGATTTGGCGGAACAA
GTT

Alignment

ORF - retro_ecab_547 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLYDDLGVETSDSKTEGWSKNFKLLQSQLQVKKAALTQAKSQRTKQSTVLAPVIDLKRAGSSDDRQIVD
          MSLYDDLGVETSDSKTEGWSKNF.LLQSQLQVK.AALTQAKSQRTKQSTVLAPVIDLKR.GSSDDRQIVD
Retrocopy MSLYDDLGVETSDSKTEGWSKNFTLLQSQLQVKRAALTQAKSQRTKQSTVLAPVIDLKRGGSSDDRQIVD

Parental  TPPHAAAGLKDPVPSGFSAGEVLIPLADEYDPMFPNDYEKVVKRQREERQRQRELERQKEIEEREKRRKD
          TPPH.AAGLKDPVPSGFSAGEVLIPLADEYDP.FPNDYEKVVKRQREERQRQRELERQKEIEEREKRRKD
Retrocopy TPPHVAAGLKDPVPSGFSAGEVLIPLADEYDPRFPNDYEKVVKRQREERQRQRELERQKEIEEREKRRKD

Parental  RHEASGFSRRPDPDSDEDEDYERERRKRSMGGAAIAPPTSLVEKDKELPRDFPYEEDSRPRSQSSKAAIP
          RHEASGFSRR.DPDSDEDEDYERERRKRSMGGAAI.PPTSLVEKDKELPRDFP.EEDSRPRSQSSKA.IP
Retrocopy RHEASGFSRRTDPDSDEDEDYERERRKRSMGGAAITPPTSLVEKDKELPRDFPHEEDSRPRSQSSKAGIP

Parental  PPVYEEQDRPRSPTGPGNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKIIVG
          PPVYEEQD.PRSPTGPGNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLS.ALSVEKTSKRGGKIIVG
Retrocopy PPVYEEQDKPRSPTGPGNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSMALSVEKTSKRGGKIIVG

Parental  DATEKDAAKKSDSNPLTEILKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDD
          DATEKDAAKKSDSNPLTE............NMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEI.GAPDD
Retrocopy DATEKDAAKKSDSNPLTEXXXXXXXXXXXXNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEILGAPDD

Parental  EAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDKFRVLDLAEQV
          EAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDKFRVLDLAEQV
Retrocopy EAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDKFRVLDLAEQV

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
SRP021940_articular_cartilage	1.24 RPM	11.86 RPM
SRP021940_cerebellum	0.62 RPM	16.00 RPM
SRP021940_embryo	1.02 RPM	26.57 RPM
SRP021940_placental_villous	0.82 RPM	15.01 RPM
SRP021940_synovial_membrane	1.13 RPM	16.28 RPM
SRP021940_testis	1.60 RPM	56.97 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_547 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_547 has 0 orthologous retrocopies within eutheria group .

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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,