RetrogeneDB ID: retro_ptro_2909

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:100428953..100429496(-)
• Located in intron of: ENSPTRG00000023608

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000041941
• Aliases: None
• Description: None

Sequence

>retro_ptro_2909
CCTGTGAGCCGTGGCCGTTGCCAGATGTCCACAATGGGAAACGAGGCCAGTTACCCGGCGGAGATGTGCTCCCACTTTGA
CAATGATGAAATTAAAAGGCTGGGCAGGAGGTTTAAGAAGTTGGACTTGGACAAATCAGGGTCTCTGAGCGTGGAGGAGT
TCATGTCCCTGCCGGAGCTGCGCCACAACCCGTTGGTGCGGCGAGTGATCGACGTCTTCGACACCGACGGTGATGGAGAA
GTGGACTTCAAGGAATTCATCCTGGGGACCTCCCAGTTCAGCGTCAAGGGCAACGAGGAGCAGAAGTTGAGGTTTGCGTT
CAGCATTTACGACATGGATAAAGATGGCTACATTTCCAACGGGGAGCTCTTCCAGGTGCTGAAGATGATGGTGGGCAACA
ACCTGACGGACTGGCAGCTCCAGCAGCTGGTCGACAAAACCATCATCATCCTGGACAAGGATGGCGATGGGAAGATATCC
TTTGAGGAATTCAGTGCTGTGGTCAGAGACCTGGAGATCCACAAGAAGCTGGTCCTCATCGTG

Alignment

ORF - retro_ptro_2909 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 97.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLRRESCGMELCGKKGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQ
          P..R..C.M......GNEASYP.EMCSHFD.DEIKRLG.RFKKLDLD.SGSLSVEEFMSLPEL..NPLV.
Retrocopy PVSRGRCQMSTM---GNEASYPAEMCSHFDNDEIKRLGRRFKKLDLDKSGSLSVEEFMSLPELRHNPLVR

Parental  RVIDIFDTDGNGEVDFKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKD
          RVID.FDTDG.GEVDFKEFI.G.SQFSVKG..EQKLRFAF.IYDMDKDGYISNGELFQVLKMMVGNNL.D
Retrocopy RVIDVFDTDGDGEVDFKEFILGTSQFSVKGNEEQKLRFAFSIYDMDKDGYISNGELFQVLKMMVGNNLTD

Parental  TQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLDIHKKMVVDV
          .QLQQ.VDKTII..DKDGDG.ISFEEF.AVV..L.IHKK.V..V
Retrocopy WQLQQLVDKTIIILDKDGDGKISFEEFSAVVRDLEIHKKLVLIV

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	85.89 RPM
SRP007412_cerebellum	0.04 RPM	78.22 RPM
SRP007412_heart	0.17 RPM	12.30 RPM
SRP007412_kidney	0.08 RPM	10.75 RPM
SRP007412_liver	0.03 RPM	13.32 RPM
SRP007412_testis	292.12 RPM	14.86 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2909 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2909 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2909 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3
Macaca mulatta	retro_mmul_1141
Callithrix jacchus	retro_cjac_624
Oryctolagus cuniculus	retro_ocun_272
Bos taurus	retro_btau_1660
Sus scrofa	retro_sscr_86
Equus caballus	retro_ecab_651

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010619	1 retrocopy	retro_btau_1660,
Choloepus hoffmanni	ENSCHOG00000002893	1 retrocopy	retro_chof_2602,
Callithrix jacchus	ENSCJAG00000006498	1 retrocopy	retro_cjac_624,
Dipodomys ordii	ENSDORG00000019760	1 retrocopy	retro_dord_404,
Equus caballus	ENSECAG00000009627	1 retrocopy	retro_ecab_651,
Felis catus	ENSFCAG00000028482	1 retrocopy	retro_fcat_1639,
Homo sapiens	ENSG00000221823	1 retrocopy	retro_hsap_3,
Loxodonta africana	ENSLAFG00000022682	1 retrocopy	retro_lafr_1014,
Macaca mulatta	ENSMMUG00000017460	1 retrocopy	retro_mmul_1141,
Mustela putorius furo	ENSMPUG00000006250	1 retrocopy	retro_mputfur_537,
Nomascus leucogenys	ENSNLEG00000026538	1 retrocopy	retro_nleu_1049,
Oryctolagus cuniculus	ENSOCUG00000027562	1 retrocopy	retro_ocun_272,
Otolemur garnettii	ENSOGAG00000034876	1 retrocopy	retro_ogar_1011,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144, retro_ptro_2407,
Pan troglodytes	ENSPTRG00000041941	1 retrocopy	retro_ptro_2909 ,
Rattus norvegicus	ENSRNOG00000043210	1 retrocopy	retro_rnor_1932,
Sus scrofa	ENSSSCG00000022362	1 retrocopy	retro_sscr_86,
Ictidomys tridecemlineatus	ENSSTOG00000025985	1 retrocopy	retro_itri_1569,
Tarsius syrichta	ENSTSYG00000019531	2 retrocopies	retro_tsyr_326, retro_tsyr_41,
Tursiops truncatus	ENSTTRG00000021395	1 retrocopy	retro_ttru_382,
Vicugna pacos	ENSVPAG00000015522	1 retrocopy	retro_vpac_3,
Drosophila melanogaster	FBgn0015614	1 retrocopy	retro_dmel_53,