RetrogeneDB ID: retro_ptro_2440

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:70389210..70389495(-)
• Located in intron of: ENSPTRG00000018327

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL37
• Ensembl ID: ENSPTRG00000016822
• Aliases: None
• Description: Pan troglodytes ribosomal protein L37 (RPL37), mRNA. [Source:RefSeq mRNA;Acc:NM_001246471]

Sequence

>retro_ptro_2440
AAGGGAACGCCATCGTTTGAAAAGTGTCTCAATAAGACGCACACATTGTGCCACCACTGTGGCTCTAAGGCCTGCCACCT
TCAGAGGTCATCCTGTGGCAAATGTGGCTACCCTGCTAAGTGCAAGAGGAAGTATAACTGAAGTGCCAAGGCTTAAAGAT
GAAATAATACCAGGACTGGTCGAGTGAGGCACCTGAATATTGTATACCGCAGATTCAGGCGTGGATTCTGAGAAGGAACA
ACATCTAAACCCAAGAGGGCAGCTGTTGTAGCATCCAGTTTATCT

Alignment

ORF - retro_ptro_2440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.84 %
• Parental protein coverage: 97.94 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGRMRHLKIVYR
          KGT.SF.K..NKTHTLC..CGSKA.HLQ.S.CGKCGYPAK.KRKYN.SAKA.R.N.T.TGR.RHL.IVYR
Retrocopy KGTPSFEKCLNKTHTLCHHCGSKACHLQRSSCGKCGYPAKCKRKYN*SAKA*R*NNTRTGRVRHLNIVYR

Parental  RFRHGFREGTTPKPKRAAVAASSSS
          RFR.GF.EGTT.KPKRAAV.ASS.S
Retrocopy RFRRGF*EGTTSKPKRAAVVASSLS

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	186.20 RPM
SRP007412_cerebellum	0.00 RPM	129.27 RPM
SRP007412_heart	0.00 RPM	107.00 RPM
SRP007412_kidney	0.03 RPM	357.44 RPM
SRP007412_liver	0.00 RPM	210.97 RPM
SRP007412_testis	0.00 RPM	46.90 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2440 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2440 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3610
Gorilla gorilla	retro_ggor_2436
Pongo abelii	retro_pabe_2962

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 117 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145592	21 retrocopies	retro_hsap_1277, retro_hsap_1424, retro_hsap_156, retro_hsap_1747, retro_hsap_1763, retro_hsap_2009, retro_hsap_2120, retro_hsap_2239, retro_hsap_2265, retro_hsap_2499, retro_hsap_2515, retro_hsap_2923, retro_hsap_343, retro_hsap_3610, retro_hsap_3901, retro_hsap_3958, retro_hsap_4685, retro_hsap_537, retro_hsap_795, retro_hsap_887, retro_hsap_953,
Latimeria chalumnae	ENSLACG00000002787	1 retrocopy	retro_lcha_6,
Loxodonta africana	ENSLAFG00000030052	13 retrocopies	retro_lafr_1101, retro_lafr_1123, retro_lafr_1125, retro_lafr_1136, retro_lafr_215, retro_lafr_374, retro_lafr_448, retro_lafr_507, retro_lafr_532, retro_lafr_619, retro_lafr_775, retro_lafr_985, retro_lafr_986,
Myotis lucifugus	ENSMLUG00000001565	10 retrocopies	retro_mluc_1037, retro_mluc_1334, retro_mluc_1441, retro_mluc_1651, retro_mluc_1897, retro_mluc_1917, retro_mluc_2006, retro_mluc_454, retro_mluc_738, retro_mluc_959,
Macaca mulatta	ENSMMUG00000023807	6 retrocopies	retro_mmul_1602, retro_mmul_1672, retro_mmul_206, retro_mmul_329, retro_mmul_976, retro_mmul_997,
Monodelphis domestica	ENSMODG00000020301	3 retrocopies	retro_mdom_130, retro_mdom_1843, retro_mdom_942,
Nomascus leucogenys	ENSNLEG00000016508	4 retrocopies	retro_nleu_1841, retro_nleu_2065, retro_nleu_2407, retro_nleu_77,
Otolemur garnettii	ENSOGAG00000034300	7 retrocopies	retro_ogar_127, retro_ogar_1308, retro_ogar_1662, retro_ogar_1667, retro_ogar_2670, retro_ogar_662, retro_ogar_76,
Pongo abelii	ENSPPYG00000015422	26 retrocopies	retro_pabe_1058, retro_pabe_1180, retro_pabe_1443, retro_pabe_1532, retro_pabe_1643, retro_pabe_1705, retro_pabe_1756, retro_pabe_1840, retro_pabe_1851, retro_pabe_1865, retro_pabe_1951, retro_pabe_1967, retro_pabe_1985, retro_pabe_212, retro_pabe_2403, retro_pabe_2432, retro_pabe_2962, retro_pabe_3180, retro_pabe_3260, retro_pabe_353, retro_pabe_3549, retro_pabe_3638, retro_pabe_466, retro_pabe_634, retro_pabe_707, retro_pabe_813,
Pan troglodytes	ENSPTRG00000016822	20 retrocopies	retro_ptro_1208, retro_ptro_1219, retro_ptro_1338, retro_ptro_1451, retro_ptro_1460, retro_ptro_152, retro_ptro_1552, retro_ptro_1584, retro_ptro_1605, retro_ptro_1978, retro_ptro_2440 , retro_ptro_2654, retro_ptro_2687, retro_ptro_273, retro_ptro_403, retro_ptro_553, retro_ptro_613, retro_ptro_660, retro_ptro_873, retro_ptro_974,
Rattus norvegicus	ENSRNOG00000012538	6 retrocopies	retro_rnor_171, retro_rnor_181, retro_rnor_220, retro_rnor_246, retro_rnor_321, retro_rnor_325,