RetrogeneDB ID: retro_ptro_2953

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03173476.1:1054..1471(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS16
• Ensembl ID: ENSPTRG00000010970
• Aliases: None
• Description: ribosomal protein S16 [Source:HGNC Symbol;Acc:10396]

Sequence

>retro_ptro_2953
CAGTCGGTGCGGGTCTTTGGACGCAAGAAGACAGCCACAGCTGTGGCGCACTGCAAACGCGGCAGTGGTCTCATGAAGGT
GAACGGGCGGCCCCTGGAGATGATTGAGCCGCTCACGCTACAGTACAAGCTGCTGGAGCCAGTTCTGCTTCTCAGCAAGG
AGCGATTTGCTGGTGTGGACTTTCGTGTCCGTGTGGAGGGTGGTGGTCATGTGGCCCAGATTTATGCTACCCGTCAGTCC
ATCTCCAAAGCCCTGGTGGCCTATTACCAGAAGTATATGGATGAGGCTTCCAAGAAGGAGATAAAAGACATCCTCATCCT
GTATGACCAGACCCTGCTGGTAGCTGATCCCCGTCCCTGCGAGTCCAAAAAGTTTAGAGGCCCTGGTGCCTGTGCTCACT
ACTAGAAATCCTACCGA

Alignment

ORF - retro_ptro_2953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.49 %
• Parental protein coverage: 95.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDIRVRVKGGGH
          QSV.VFGRKKTATAVAHCKRG.GL.KVNGRPLEMIEP.TLQYKLLEPVLLL.KERFAGVD.RVRV.GGGH
Retrocopy QSVRVFGRKKTATAVAHCKRGSGLMKVNGRPLEMIEPLTLQYKLLEPVLLLSKERFAGVDFRVRVEGGGH

Parental  VAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVADPRRCESKKFGGPGARARYQKSYR
          VAQIYA.RQSISKALVAYYQKY.DEASKKEIKDILI.YD.TLLVADPR.CESKKF.GPGA.A.Y.KSYR
Retrocopy VAQIYATRQSISKALVAYYQKYMDEASKKEIKDILILYDQTLLVADPRPCESKKFRGPGACAHY*KSYR

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	0.11 RPM	216.57 RPM
SRP007412_cerebellum	0.54 RPM	203.40 RPM
SRP007412_heart	0.00 RPM	172.46 RPM
SRP007412_kidney	0.05 RPM	372.58 RPM
SRP007412_liver	0.03 RPM	365.87 RPM
SRP007412_testis	0.21 RPM	58.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2953 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2953 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2953 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014176	1 retrocopy	retro_acar_194,
Bos taurus	ENSBTAG00000021093	3 retrocopies	retro_btau_1509, retro_btau_167, retro_btau_441,
Callithrix jacchus	ENSCJAG00000014170	6 retrocopies	retro_cjac_2641, retro_cjac_2737, retro_cjac_3019, retro_cjac_885, retro_cjac_905, retro_cjac_949,
Cavia porcellus	ENSCPOG00000011359	3 retrocopies	retro_cpor_1266, retro_cpor_1408, retro_cpor_1515,
Dasypus novemcinctus	ENSDNOG00000001527	3 retrocopies	retro_dnov_2260, retro_dnov_2315, retro_dnov_308,
Echinops telfairi	ENSETEG00000015290	4 retrocopies	retro_etel_1825, retro_etel_1834, retro_etel_193, retro_etel_351,
Felis catus	ENSFCAG00000010743	4 retrocopies	retro_fcat_1258, retro_fcat_1709, retro_fcat_1806, retro_fcat_1976,
Gorilla gorilla	ENSGGOG00000014414	10 retrocopies	retro_ggor_110, retro_ggor_1250, retro_ggor_1344, retro_ggor_1664, retro_ggor_1766, retro_ggor_193, retro_ggor_2423, retro_ggor_2819, retro_ggor_652, retro_ggor_667,
Macropus eugenii	ENSMEUG00000010380	2 retrocopies	retro_meug_1306, retro_meug_612,
Microcebus murinus	ENSMICG00000006110	4 retrocopies	retro_mmur_1006, retro_mmur_1058, retro_mmur_375, retro_mmur_798,
Macaca mulatta	ENSMMUG00000019370	8 retrocopies	retro_mmul_1018, retro_mmul_1080, retro_mmul_1175, retro_mmul_1219, retro_mmul_1403, retro_mmul_20, retro_mmul_767, retro_mmul_862,
Nomascus leucogenys	ENSNLEG00000014388	3 retrocopies	retro_nleu_1266, retro_nleu_248, retro_nleu_46,
Otolemur garnettii	ENSOGAG00000004497	4 retrocopies	retro_ogar_1229, retro_ogar_1309, retro_ogar_1313, retro_ogar_98,
Oreochromis niloticus	ENSONIG00000000006	1 retrocopy	retro_onil_52,
Pelodiscus sinensis	ENSPSIG00000016930	1 retrocopy	retro_psin_55,
Pan troglodytes	ENSPTRG00000010970	11 retrocopies	retro_ptro_1223, retro_ptro_1318, retro_ptro_1376, retro_ptro_1577, retro_ptro_1699, retro_ptro_2432, retro_ptro_2857, retro_ptro_2953 , retro_ptro_2957, retro_ptro_548, retro_ptro_565,
Rattus norvegicus	ENSRNOG00000019578	3 retrocopies	retro_rnor_10, retro_rnor_1823, retro_rnor_302,
Sorex araneus	ENSSARG00000000852	1 retrocopy	retro_sara_595,
Sus scrofa	ENSSSCG00000010712	1 retrocopy	retro_sscr_731,
Sus scrofa	ENSSSCG00000020817	3 retrocopies	retro_sscr_478, retro_sscr_5, retro_sscr_723,
Tarsius syrichta	ENSTSYG00000005241	4 retrocopies	retro_tsyr_1115, retro_tsyr_1208, retro_tsyr_1492, retro_tsyr_1780,
Tursiops truncatus	ENSTTRG00000003571	1 retrocopy	retro_ttru_202,