RetrogeneDB ID: retro_ptro_2878

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:19490061..19490526(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS6
• Ensembl ID: ENSPTRG00000039153
• Aliases: None
• Description: ribosomal protein S6 [Source:HGNC Symbol;Acc:10429]

Sequence

>retro_ptro_2878
ATGAAGCTGAACATCTCCTTCCCAGCCACTGGCTGCCAGAAACTCATTGAAGTGGATGATGAATGCAAACTTCGTACTTT
TTATGAGAAACGTACGGCCACAAAAGTTGCTGCTGACACACTGGGTGAAGAATGGAAGGGTTATGTGGTCCGAATCAGTG
GTGGGAACGACAAATAAGGTTTCCCCATGAAGCAGGGTGTCTTGACCCACGGCCGTGTCCACTTGCTACTGAGTAAGGGG
CATTCCTGTTACAGACCAAGGAGAACTGGAGAAAGAAAGGGAAAATCAGTTCATGGTTGCATTGTGATTGCCAATCTGAG
CATTCTCAACTTGGTTATTGTAAAAAAAGGAGAGAAGGATATTCCTGGACTGACTGATACTATGGTGCCTCATCACCTGG
GACCCAAAAGAGCTAGCAGAATCCATAAACTTTTCAATCTCTCTAAAGAAAGCCCTTAAAGAAGG

Alignment

ORF - retro_ptro_2878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.39 %
• Parental protein coverage: 62.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTH
          MKLNISFPATGCQKLIEVDDE.KLRTFYEKR.AT.VAAD.LGEEWKGYVVRISGGNDK.GFPMKQGVLTH
Retrocopy MKLNISFPATGCQKLIEVDDECKLRTFYEKRTATKVAADTLGEEWKGYVVRISGGNDK*GFPMKQGVLTH

Parental  GRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASR
          GRV.LLLSKGHSCYRPRRTGERK.KSV.GCIV.ANLS.LNLVIVKKGEKDIPGLTDT.VP..LGPKRASR
Retrocopy GRVHLLLSKGHSCYRPRRTGERKGKSVHGCIVIANLSILNLVIVKKGEKDIPGLTDTMVPHHLGPKRASR

Parental  IRKLFNLSKEDDVRQ
          I.KLFNLSKE...R.
Retrocopy IHKLFNLSKESP*RR

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	0.45 RPM	181.85 RPM
SRP007412_cerebellum	0.07 RPM	243.66 RPM
SRP007412_heart	0.03 RPM	222.04 RPM
SRP007412_kidney	0.29 RPM	476.98 RPM
SRP007412_liver	0.07 RPM	310.75 RPM
SRP007412_testis	0.42 RPM	256.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2878 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2878 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4235

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 122 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Echinops telfairi	ENSETEG00000001584	18 retrocopies	retro_etel_1143, retro_etel_1281, retro_etel_1410, retro_etel_1430, retro_etel_1575, retro_etel_167, retro_etel_1822, retro_etel_188, retro_etel_1964, retro_etel_2004, retro_etel_2041, retro_etel_2194, retro_etel_263, retro_etel_337, retro_etel_378, retro_etel_541, retro_etel_809, retro_etel_825,
Homo sapiens	ENSG00000137154	16 retrocopies	retro_hsap_1009, retro_hsap_1067, retro_hsap_1231, retro_hsap_1310, retro_hsap_1967, retro_hsap_2184, retro_hsap_2298, retro_hsap_3045, retro_hsap_3996, retro_hsap_4122, retro_hsap_4235, retro_hsap_4279, retro_hsap_4860, retro_hsap_731, retro_hsap_818, retro_hsap_966,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Myotis lucifugus	ENSMLUG00000007588	27 retrocopies	retro_mluc_1041, retro_mluc_1146, retro_mluc_1169, retro_mluc_1393, retro_mluc_1411, retro_mluc_1448, retro_mluc_1472, retro_mluc_1532, retro_mluc_1566, retro_mluc_1593, retro_mluc_1629, retro_mluc_1635, retro_mluc_1723, retro_mluc_1799, retro_mluc_1909, retro_mluc_1928, retro_mluc_1933, retro_mluc_2110, retro_mluc_2129, retro_mluc_490, retro_mluc_493, retro_mluc_514, retro_mluc_557, retro_mluc_652, retro_mluc_678, retro_mluc_722, retro_mluc_830,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Pan troglodytes	ENSPTRG00000039153	19 retrocopies	retro_ptro_1313, retro_ptro_1442, retro_ptro_1627, retro_ptro_1662, retro_ptro_1994, retro_ptro_2442, retro_ptro_2713, retro_ptro_2799, retro_ptro_2878 , retro_ptro_2902, retro_ptro_2938, retro_ptro_3235, retro_ptro_519, retro_ptro_569, retro_ptro_669, retro_ptro_749, retro_ptro_785, retro_ptro_799, retro_ptro_845,
Rattus norvegicus	ENSRNOG00000007663	21 retrocopies	retro_rnor_1092, retro_rnor_1093, retro_rnor_1269, retro_rnor_1484, retro_rnor_1556, retro_rnor_1564, retro_rnor_1845, retro_rnor_1901, retro_rnor_1991, retro_rnor_2071, retro_rnor_2073, retro_rnor_2187, retro_rnor_2332, retro_rnor_2447, retro_rnor_2781, retro_rnor_2790, retro_rnor_558, retro_rnor_756, retro_rnor_896, retro_rnor_942, retro_rnor_943,
Sorex araneus	ENSSARG00000006549	6 retrocopies	retro_sara_284, retro_sara_369, retro_sara_392, retro_sara_436, retro_sara_512, retro_sara_710,