RetrogeneDB ID: retro_pabe_529

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:59774655..59775106(+)
• Located in intron of: ENSPPYG00000002313

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPA17
• Ensembl ID: ENSPPYG00000004017
• Aliases: None
• Description: sperm autoantigenic protein 17 [Source:HGNC Symbol;Acc:11210]

Sequence

>retro_pabe_529
ATGTCGATTCCATTCTCCAACACCCACTACTGAATTCTGCAAGGATTTGGGAGTCTTCTTGAAGAGCTGACCCACGAGAT
TCTGAGAGAGCAACCAGATAATATACAGCTTTTTCAGCAACATATTTTGAGAGCTTTCCAGAGAAAAGAGAGAAAACCAC
TTTTGATCCAGCAGAATGGGGGACTCAGGTAGAAGACCGATTCTAGAACAGTCATGCATTCGAGGAGCAAGAACCACCTG
AGAAATGTGATCCTAAACAAGAAAACTCTCCAGTATCTGGGAAGGAGGAAGAGACACCAGTCACCATCTTAGACTCTTCT
GAGGAAGACAAGGAAAAAGAAGAGGTGCTGCTGTCAAAATCCAAGCTGCCTTCTGGGGACACACAGCCAGAGAGGAGGTA
AAGAGAATGAAAACAGACAGTCTCCGACATCAGGAAACAGAGGAAAACAAG

Alignment

ORF - retro_pabe_529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSIPFSNTHYRIPQGFGNLLEGLTREILREQPDNIP-AFAAAYFESLLEKREKTNFDPAEWGSKVEDRFY
          MSIPFSNTHY.I.QGFG.LLE.LT.EILREQPDNI..AF.A.YFES..EKREKT.FDPAEWG..VEDRF.
Retrocopy MSIPFSNTHY*ILQGFGSLLEELTHEILREQPDNIQ<AFSATYFESFPEKREKTTFDPAEWGTQVEDRF*

Parental  NNHAFEEQEPPEKSDPKQEESQISRKEEEISITILDSSEEDKEKEEV-AAVKIQAAFRGHIAREEAKKMK
          N.HAFEEQEPPEK.DPKQE.S..S.KEEE...TILDSSEEDKEKEEV.AAVKIQAAF.GH.AREE.K.MK
Retrocopy NSHAFEEQEPPEKCDPKQENSPVSGKEEETPVTILDSSEEDKEKEEV<AAVKIQAAFWGHTAREEVKRMK

Parental  TNSLQNEEKEENK
          T.SL...E.EENK
Retrocopy TDSLRHQETEENK

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	1.94 RPM
SRP007412_cerebellum	0.00 RPM	0.97 RPM
SRP007412_heart	0.00 RPM	0.27 RPM
SRP007412_kidney	0.20 RPM	4.18 RPM
SRP007412_liver	0.00 RPM	0.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_529 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_529 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_529 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_696
Pan troglodytes	retro_ptro_500
Gorilla gorilla	retro_ggor_593
Macaca mulatta	retro_mmul_2405
Callithrix jacchus	retro_cjac_978

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007961	1 retrocopy	retro_cjac_978,
Echinops telfairi	ENSETEG00000007789	1 retrocopy	retro_etel_911,
Homo sapiens	ENSG00000064199	1 retrocopy	retro_hsap_696,
Gorilla gorilla	ENSGGOG00000003757	1 retrocopy	retro_ggor_593,
Macaca mulatta	ENSMMUG00000008480	1 retrocopy	retro_mmul_2405,
Nomascus leucogenys	ENSNLEG00000007436	1 retrocopy	retro_nleu_2229,
Pongo abelii	ENSPPYG00000004017	1 retrocopy	retro_pabe_529 ,
Pan troglodytes	ENSPTRG00000004426	1 retrocopy	retro_ptro_500,
Tarsius syrichta	ENSTSYG00000008379	1 retrocopy	retro_tsyr_2091,