RetrogeneDB ID: retro_ptro_1494

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:41845418..41845780(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS25
• Ensembl ID: ENSPTRG00000004361
• Aliases: None
• Description: Pan troglodytes ribosomal protein S25 (RPS25), mRNA. [Source:RefSeq mRNA;Acc:NM_001251993]

Sequence

>retro_ptro_1494
AAGGATGACAAGAAGAACGAAGACACCGGAAAGTCGCTAAGAAAGACAAAGATTCAGTGAACAAATCTGGGGGCAGGGCC
CAAAAGAAGAAGTGGTCCAAAGGCAAAGTCCGGGACAAGCTCAATAACTGAGTCGTGTTTGACAAACCTACCTATGACAA
ACTCTGTAAGGAAGTTCCCAACCATAAACTTATAAGCCCTGCTGTGGTCTCTGAGAAACTGAAGATTCGAGGCTTCCTGG
CCAGGGCAGCCCTTCAGGAGAACCTTAGTAAAGGACTTAACAAACTGGTTTCAAAGCACAGAGCTCAAGTAATTTACATC
AGAAATACCAAGGGTGAAGATGTTATAGCTGCTGGTGATGAT

Alignment

ORF - retro_ptro_1494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.79 %
• Parental protein coverage: 96.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDDKKKKDAGKS-AKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITPAV
          KDDKK..D.GKS.AKKDKD.VNKSGG.A.KKKWSKGKVRDKLNN.V.FDK.TYDKLCKEVPN.KLI.PAV
Retrocopy KDDKKNEDTGKS<AKKDKDSVNKSGGRAQKKKWSKGKVRDKLNN*VVFDKPTYDKLCKEVPNHKLISPAV

Parental  VSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGED
          VSE.LKIRG.LARAALQE.LSKGL.KLVSKHRAQVIY.RNTKG.D..AAG.D
Retrocopy VSEKLKIRGFLARAALQENLSKGLNKLVSKHRAQVIYIRNTKGEDVIAAGDD

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	64.85 RPM
SRP007412_cerebellum	0.04 RPM	55.74 RPM
SRP007412_heart	0.00 RPM	84.12 RPM
SRP007412_kidney	0.05 RPM	127.65 RPM
SRP007412_liver	0.00 RPM	95.88 RPM
SRP007412_testis	0.32 RPM	59.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1494 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1494 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1494 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2563
Gorilla gorilla	retro_ggor_1601
Pongo abelii	retro_pabe_1889

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 84 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027772	2 retrocopies	retro_btau_203, retro_btau_9,
Callithrix jacchus	ENSCJAG00000013691	1 retrocopy	retro_cjac_208,
Dasypus novemcinctus	ENSDNOG00000007880	7 retrocopies	retro_dnov_1092, retro_dnov_1566, retro_dnov_2219, retro_dnov_2593, retro_dnov_346, retro_dnov_877, retro_dnov_973,
Mus musculus	ENSMUSG00000009927	15 retrocopies	retro_mmus_128, retro_mmus_1368, retro_mmus_1455, retro_mmus_1760, retro_mmus_1769, retro_mmus_1788, retro_mmus_2375, retro_mmus_2393, retro_mmus_2641, retro_mmus_2700, retro_mmus_2797, retro_mmus_3218, retro_mmus_336, retro_mmus_3523, retro_mmus_880,
Oryctolagus cuniculus	ENSOCUG00000017256	11 retrocopies	retro_ocun_1166, retro_ocun_1231, retro_ocun_1319, retro_ocun_1553, retro_ocun_1761, retro_ocun_291, retro_ocun_298, retro_ocun_548, retro_ocun_623, retro_ocun_856, retro_ocun_978,
Otolemur garnettii	ENSOGAG00000007265	3 retrocopies	retro_ogar_220, retro_ogar_257, retro_ogar_32,
Pan troglodytes	ENSPTRG00000004361	10 retrocopies	retro_ptro_1368, retro_ptro_1494 , retro_ptro_1579, retro_ptro_1722, retro_ptro_1935, retro_ptro_2291, retro_ptro_2411, retro_ptro_245, retro_ptro_2918, retro_ptro_536,
Sorex araneus	ENSSARG00000002284	4 retrocopies	retro_sara_21, retro_sara_212, retro_sara_43, retro_sara_542,
Tupaia belangeri	ENSTBEG00000010244	16 retrocopies	retro_tbel_1592, retro_tbel_1823, retro_tbel_1849, retro_tbel_22, retro_tbel_2651, retro_tbel_2744, retro_tbel_3106, retro_tbel_3107, retro_tbel_3499, retro_tbel_374, retro_tbel_3871, retro_tbel_3877, retro_tbel_4239, retro_tbel_4434, retro_tbel_444, retro_tbel_4464,
Tarsius syrichta	ENSTSYG00000005422	15 retrocopies	retro_tsyr_1050, retro_tsyr_1098, retro_tsyr_1125, retro_tsyr_1230, retro_tsyr_1252, retro_tsyr_1454, retro_tsyr_154, retro_tsyr_1558, retro_tsyr_2081, retro_tsyr_358, retro_tsyr_414, retro_tsyr_428, retro_tsyr_570, retro_tsyr_859, retro_tsyr_873,