RetrogeneDB ID: retro_ptro_399

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:220655898..220656177(-)
• Located in intron of: ENSPTRG00000002161

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL36
• Ensembl ID: ENSPTRG00000010338
• Aliases: None
• Description: Pan troglodytes ribosomal protein L36 (RPL36), mRNA. [Source:RefSeq mRNA;Acc:NM_001252514]

Sequence

>retro_ptro_399
ATGGTCCTGCACTACCCCATGGCCGTGGGCCTCAACAAAGGCCACAAGGTGACCAAGAACGTGAGGAAACCAAGGCACAG
CCAAGCAGGCGCCTCAGCAAACACCAAAATCGCTCGAGACATGCCCCGAGAGGTGTGTGGCTTTGTTCCATAGAGCGGTG
TGCTGTGGAGTTGCTCAAGCTCTCCCAGGACAAACAGGCCCTCAAATTCATCAGGAAAAGGGTGGGGGGCACACTTCCCC
CCCAAGAGAAAGTGAGAGAGCCTGTGCAATGTCCCGGCC

Alignment

ORF - retro_ptro_399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.98 %
• Parental protein coverage: 90.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALRYPMAVGLNKGHKVTKNVSKPRHSRRRGRLTKHTKFVRDMIREVCGFAP-YERRAMELLKVSKDKRA
          M.L.YPMAVGLNKGHKVTKNV.KPRHS.........TK..RDM.REVCGF.P..ER.A.ELLK.S.DK.A
Retrocopy MVLHYPMAVGLNKGHKVTKNVRKPRHS--QAGASANTKIARDMPREVCGFVP<IERCAVELLKLSQDKQA

Parental  LKFIKKRV-GTHIRAKRKREELSNVLA
          LKFI.KRV.G.H...KRK.E.L.NV.A
Retrocopy LKFIRKRV>GAHFPPKRK*ESLCNVPA

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	127.02 RPM
SRP007412_cerebellum	0.14 RPM	50.22 RPM
SRP007412_heart	0.00 RPM	23.58 RPM
SRP007412_kidney	0.00 RPM	157.46 RPM
SRP007412_liver	0.00 RPM	102.95 RPM
SRP007412_testis	0.00 RPM	7.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_399 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_399 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_534
Gorilla gorilla	retro_ggor_487
Pongo abelii	retro_pabe_216

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 107 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012349	6 retrocopies	retro_amel_1222, retro_amel_1581, retro_amel_1935, retro_amel_748, retro_amel_799, retro_amel_835,
Bos taurus	ENSBTAG00000001794	3 retrocopies	retro_btau_139, retro_btau_238, retro_btau_81,
Callithrix jacchus	ENSCJAG00000017072	2 retrocopies	retro_cjac_280, retro_cjac_52,
Dasypus novemcinctus	ENSDNOG00000005163	8 retrocopies	retro_dnov_19, retro_dnov_2160, retro_dnov_311, retro_dnov_313, retro_dnov_457, retro_dnov_578, retro_dnov_595, retro_dnov_631,
Gorilla gorilla	ENSGGOG00000015365	11 retrocopies	retro_ggor_1514, retro_ggor_1613, retro_ggor_180, retro_ggor_2211, retro_ggor_2535, retro_ggor_2620, retro_ggor_34, retro_ggor_487, retro_ggor_60, retro_ggor_82, retro_ggor_885,
Latimeria chalumnae	ENSLACG00000015161	1 retrocopy	retro_lcha_47,
Macropus eugenii	ENSMEUG00000002743	4 retrocopies	retro_meug_1318, retro_meug_176, retro_meug_261, retro_meug_283,
Monodelphis domestica	ENSMODG00000001275	2 retrocopies	retro_mdom_1353, retro_mdom_148,
Mustela putorius furo	ENSMPUG00000006166	6 retrocopies	retro_mputfur_1423, retro_mputfur_150, retro_mputfur_1562, retro_mputfur_747, retro_mputfur_749, retro_mputfur_773,
Mus musculus	ENSMUSG00000057863	9 retrocopies	retro_mmus_151, retro_mmus_1601, retro_mmus_1900, retro_mmus_1912, retro_mmus_193, retro_mmus_2864, retro_mmus_3379, retro_mmus_38, retro_mmus_652,
Nomascus leucogenys	ENSNLEG00000013689	15 retrocopies	retro_nleu_1132, retro_nleu_1244, retro_nleu_1415, retro_nleu_1645, retro_nleu_1699, retro_nleu_1788, retro_nleu_183, retro_nleu_1899, retro_nleu_2032, retro_nleu_2123, retro_nleu_242, retro_nleu_2451, retro_nleu_2503, retro_nleu_2835, retro_nleu_757,
Otolemur garnettii	ENSOGAG00000027049	12 retrocopies	retro_ogar_1348, retro_ogar_18, retro_ogar_184, retro_ogar_2256, retro_ogar_2278, retro_ogar_2332, retro_ogar_2537, retro_ogar_2592, retro_ogar_3278, retro_ogar_358, retro_ogar_795, retro_ogar_888,
Pan troglodytes	ENSPTRG00000010338	13 retrocopies	retro_ptro_1334, retro_ptro_1406, retro_ptro_1430, retro_ptro_1506, retro_ptro_1989, retro_ptro_2196, retro_ptro_2555, retro_ptro_2647, retro_ptro_2858, retro_ptro_3157, retro_ptro_399 , retro_ptro_721, retro_ptro_982,
Rattus norvegicus	ENSRNOG00000033473	5 retrocopies	retro_rnor_11, retro_rnor_17, retro_rnor_170, retro_rnor_369, retro_rnor_687,
Sarcophilus harrisii	ENSSHAG00000013492	8 retrocopies	retro_shar_185, retro_shar_347, retro_shar_543, retro_shar_557, retro_shar_592, retro_shar_615, retro_shar_716, retro_shar_819,
Ictidomys tridecemlineatus	ENSSTOG00000020518	2 retrocopies	retro_itri_43, retro_itri_593,