RetrogeneDB ID: retro_ptro_1189

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:61106761..61107102(+)
• Located in intron of: ENSPTRG00000009502

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP2
• Ensembl ID: ENSPTRG00000003137
• Aliases: None
• Description: ribosomal protein, large, P2 [Source:HGNC Symbol;Acc:10377]

Sequence

>retro_ptro_1189
GTGCGCTCGGTCACCTCCCTCCTGCTGGCTGCCCTCGGGGGCAGCACCTCCCTCAGAGCCAAAGACATCAAGAGGATCCT
GGACAGCGTAGGCATCGAGGCGGACGATGACCGGCTCAACAAGTTTATCAGTGAGCTGAATGGAAAAAGCATTGAAGATG
TCATTGCCCAGGGTATTGGCAAGGTTGCCAGTGTACCTGCGGGTGGGGCTGTGGCTGTCTCTGCTGCCCCAGGCTGTGCA
GCTCCTGCTGCTGGTTCCACCCCCGCTGCAGCAGAGGAGAAGATGAGGAGGAGGAGGAGGTGTCCAAAGAGTCAGATGAT
GACATGGGATTTGGTCTCTTT

Alignment

ORF - retro_ptro_1189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.74 %
• Parental protein coverage: 99.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGA
          .R.V.S.LLAALGG..S..AKDIK.ILDSVGIEADDDRLNK.ISELNGK.IEDVIAQGIGK.ASVPAGGA
Retrocopy VRSVTSLLLAALGGSTSLRAKDIKRILDSVGIEADDDRLNKFISELNGKSIEDVIAQGIGKVASVPAGGA

Parental  VAVSAAPGSAAPAAGSAPAAAEEK-KDEKKEESEESDDDMGFGLF
          VAVSAAPG.AAPAAGS.PAAAEEK...E..E.S.ESDDDMGFGLF
Retrocopy VAVSAAPGCAAPAAGSTPAAAEEK<DEEEEEVSKESDDDMGFGLF

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	116.51 RPM
SRP007412_cerebellum	0.00 RPM	52.77 RPM
SRP007412_heart	0.03 RPM	49.05 RPM
SRP007412_kidney	0.00 RPM	175.71 RPM
SRP007412_liver	0.00 RPM	152.80 RPM
SRP007412_testis	0.00 RPM	26.77 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1189 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1189 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1189 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1777
Gorilla gorilla	retro_ggor_2238
Pongo abelii	retro_pabe_1537
Callithrix jacchus	retro_cjac_2539

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001777	2 retrocopies	retro_btau_117, retro_btau_1399,
Canis familiaris	ENSCAFG00000009523	1 retrocopy	retro_cfam_18,
Ciona intestinalis	ENSCING00000000626	1 retrocopy	retro_cint_34,
Dipodomys ordii	ENSDORG00000016458	3 retrocopies	retro_dord_705, retro_dord_706, retro_dord_707,
Felis catus	ENSFCAG00000008417	1 retrocopy	retro_fcat_860,
Homo sapiens	ENSG00000177600	5 retrocopies	retro_hsap_1777, retro_hsap_3395, retro_hsap_3440, retro_hsap_821, retro_hsap_982,
Gorilla gorilla	ENSGGOG00000010789	5 retrocopies	retro_ggor_2238, retro_ggor_2298, retro_ggor_2323, retro_ggor_672, retro_ggor_784,
Mus musculus	ENSMUSG00000025508	4 retrocopies	retro_mmus_1364, retro_mmus_2111, retro_mmus_2282, retro_mmus_330,
Nomascus leucogenys	ENSNLEG00000026860	5 retrocopies	retro_nleu_1948, retro_nleu_2144, retro_nleu_2296, retro_nleu_2762, retro_nleu_85,
Otolemur garnettii	ENSOGAG00000016296	2 retrocopies	retro_ogar_156, retro_ogar_275,
Pongo abelii	ENSPPYG00000002885	6 retrocopies	retro_pabe_1537, retro_pabe_1543, retro_pabe_2789, retro_pabe_2844, retro_pabe_732, retro_pabe_830,
Pan troglodytes	ENSPTRG00000003137	5 retrocopies	retro_ptro_1189 , retro_ptro_2307, retro_ptro_2332, retro_ptro_572, retro_ptro_764,
Rattus norvegicus	ENSRNOG00000002116	3 retrocopies	retro_rnor_257, retro_rnor_320, retro_rnor_388,
Sarcophilus harrisii	ENSSHAG00000001056	1 retrocopy	retro_shar_321,
Sus scrofa	ENSSSCG00000012842	1 retrocopy	retro_sscr_54,