RetrogeneDB ID: retro_ptro_612

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:61677063..61677498(-)
• Located in intron of: ENSPTRG00000003809

Retrocopy information

• Ensembl ID: ENSPTRG00000042420
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS19
• Ensembl ID: ENSPTRG00000011037
• Aliases: None
• Description: ribosomal protein S19 [Source:HGNC Symbol;Acc:10402]

Sequence

>retro_ptro_612
ATGCCTGGAGTTACTGTAAAAGACGTGAACCAGCAGGAGTTCGTCAGAGCTCTGGCAGCCTTCCTCAAAAAGTCCGGGAA
GCTGAAAGTCCCCGAATGGGTGGACACCGTCAAGCTGGCCAAGCACAAAGAGCTTGCTCCCTACGATGAGAACTGGTTCT
ACACGCGAGCTGCTTCCACAGCGCGGCACCTGTACCTCCGGGGTGGCGCTGGGGTTGGCTCCATGACCAAGATCTATGGG
GGACGTCAGAGAAACGGCGTCATGCCCAGCCACTTCAGCCGAGGCTCCAAGAGTGTGGCCCGCCGGGTCCTCCAAGCCCT
GGAGGGGCTGAAAATGGTGGAAAAGGACCAAGATGGCGGCCGCAAACTGACACCTCAGGGACAAAGAGATCTGGACAGAA
TCGCCGGACAGGTGGCAGCTGCCAACAAGAAGCAT

Alignment

ORF - retro_ptro_612 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGA
          MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGA
Retrocopy MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGA

Parental  GVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAA
          GVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAA
Retrocopy GVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAA

Parental  ANKKH
          ANKKH
Retrocopy ANKKH

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	3.95 RPM	63.88 RPM
SRP007412_cerebellum	0.25 RPM	20.40 RPM
SRP007412_heart	0.03 RPM	11.22 RPM
SRP007412_kidney	0.71 RPM	50.53 RPM
SRP007412_liver	1.01 RPM	57.38 RPM
SRP007412_testis	0.32 RPM	13.17 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_612 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_612 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004456	4 retrocopies	retro_amel_1418, retro_amel_1816, retro_amel_193, retro_amel_550,
Canis familiaris	ENSCAFG00000028485	10 retrocopies	retro_cfam_1017, retro_cfam_1074, retro_cfam_1155, retro_cfam_1251, retro_cfam_1377, retro_cfam_149, retro_cfam_1998, retro_cfam_2212, retro_cfam_249, retro_cfam_499,
Callithrix jacchus	ENSCJAG00000020243	5 retrocopies	retro_cjac_1968, retro_cjac_2004, retro_cjac_2094, retro_cjac_2324, retro_cjac_3,
Cavia porcellus	ENSCPOG00000025140	1 retrocopy	retro_cpor_1018,
Felis catus	ENSFCAG00000008125	3 retrocopies	retro_fcat_2026, retro_fcat_543, retro_fcat_816,
Gorilla gorilla	ENSGGOG00000015279	4 retrocopies	retro_ggor_1085, retro_ggor_1503, retro_ggor_2458, retro_ggor_578,
Myotis lucifugus	ENSMLUG00000006143	5 retrocopies	retro_mluc_1316, retro_mluc_2247, retro_mluc_2426, retro_mluc_980, retro_mluc_987,
Pongo abelii	ENSPPYG00000010029	7 retrocopies	retro_pabe_1158, retro_pabe_1754, retro_pabe_1781, retro_pabe_2636, retro_pabe_430, retro_pabe_585, retro_pabe_586,
Pan troglodytes	ENSPTRG00000011037	6 retrocopies	retro_ptro_1392, retro_ptro_2269, retro_ptro_2467, retro_ptro_485, retro_ptro_612 , retro_ptro_961,
Pteropus vampyrus	ENSPVAG00000008980	4 retrocopies	retro_pvam_1032, retro_pvam_1171, retro_pvam_137, retro_pvam_895,
Rattus norvegicus	ENSRNOG00000048199	3 retrocopies	retro_rnor_221, retro_rnor_299, retro_rnor_51,
Sarcophilus harrisii	ENSSHAG00000006831	1 retrocopy	retro_shar_731,
Sus scrofa	ENSSSCG00000003042	3 retrocopies	retro_sscr_1064, retro_sscr_308, retro_sscr_58,
Tupaia belangeri	ENSTBEG00000003457	21 retrocopies	retro_tbel_103, retro_tbel_1275, retro_tbel_1575, retro_tbel_1748, retro_tbel_1803, retro_tbel_1888, retro_tbel_2104, retro_tbel_2521, retro_tbel_2554, retro_tbel_2971, retro_tbel_3008, retro_tbel_3339, retro_tbel_3388, retro_tbel_345, retro_tbel_3607, retro_tbel_3860, retro_tbel_4425, retro_tbel_673, retro_tbel_875, retro_tbel_913, retro_tbel_945,
Tursiops truncatus	ENSTTRG00000008278	5 retrocopies	retro_ttru_1308, retro_ttru_1608, retro_ttru_1686, retro_ttru_336, retro_ttru_593,