RetrogeneDB ID: retro_ptro_500

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:73985295..73985747(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPA17
• Ensembl ID: ENSPTRG00000004426
• Aliases: None
• Description: sperm autoantigenic protein 17 [Source:HGNC Symbol;Acc:11210]

Sequence

>retro_ptro_500
ATGTCGATTCCATTCTCCAATACCCACTACTGAATTCTGCAAGGATTTGGGAGTCTTCTTAAAGAGCTGACCCACGAGAT
TCTGAGAGAGCAACCAGATAATATACAGCTTTTGCAGCAGCATATTTTGACAGCTTTCCAGAGAAAAGAGAGAAAACCAC
TTTTGATCCAGCAGAATGGGGGACTCAGGTAGAAGACTGCTTCTAGAACAGTCATGCATTCGAGGAGCAAGAACCACCTG
AGAAATGTGATCCTAAACAAGAAAACTCTCCAATATCTGGGAAGGAGGAAGAGACACCAGTCACCATCTTAGACTCTTCT
GAGGAAGATAAGGAAAAAGAAGAGGTTGCTGCTGTCAAAATCCAGGCTGCCTTCTGGGGACACACAGCCAGAGAGGAGGT
AAAAAGAATGGAAACCGATAGTCTCTGACATGAGGAAACAGAGGAATACAAG

Alignment

ORF - retro_ptro_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSIPFSNTHYRIPQGFGNLLEGLTREILREQPDNIP-AFAAAYFESLLEKREKTNFDPAEWGSKVEDRFY
          MSIPFSNTHY.I.QGFG.LL..LT.EILREQPDNI..AFAAAYF.S..EKREKT.FDPAEWG..VED.F.
Retrocopy MSIPFSNTHY*ILQGFGSLLKELTHEILREQPDNIQ<AFAAAYFDSFPEKREKTTFDPAEWGTQVEDCF*

Parental  NNHAFEEQEPPEKSDPKQEESQISGKEEETSVTILDSSEEDKEKEEVAAVKIQAAFRGHIAREEAKKMKT
          N.HAFEEQEPPEK.DPKQE.S.ISGKEEET.VTILDSSEEDKEKEEVAAVKIQAAF.GH.AREE.K.M.T
Retrocopy NSHAFEEQEPPEKCDPKQENSPISGKEEETPVTILDSSEEDKEKEEVAAVKIQAAFWGHTAREEVKRMET

Parental  NSLQNEEKEENK
          .SL..EE.EE.K
Retrocopy DSL*HEETEEYK

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	0.71 RPM
SRP007412_cerebellum	0.00 RPM	0.22 RPM
SRP007412_heart	0.06 RPM	0.38 RPM
SRP007412_kidney	0.21 RPM	2.48 RPM
SRP007412_liver	0.03 RPM	0.43 RPM
SRP007412_testis	0.32 RPM	527.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_500 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_500 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_696
Gorilla gorilla	retro_ggor_593
Pongo abelii	retro_pabe_529
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,