RetrogeneDB ID: retro_pabe_735

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:108958162..108958460(+)
• Located in intron of: ENSPPYG00000003878

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS36
• Ensembl ID: ENSPPYG00000015524
• Aliases: None
• Description: 28S ribosomal protein S36, mitochondrial [Source:RefSeq peptide;Acc:NP_001185669]

Sequence

>retro_pabe_735
ATGATGAGCAGCAAGATGCGTCTGCTAGCAGGGTCATTCAGGTAGTCAAGCCACATGCTCCATTAATAAGCTTCCCTGCT
AGAAGAGACAATCCTAAACCCAATGTACCAGAAGCTTTGAGATCTGCAGGGTAACCATCTCACGATTCTGCAATTTCCCA
GCATTCTAAGGGAAGTAAATTACTGGATTTGCGGATGTACCAGACACTGCAGAAGTAATGAAAACATTACCTCAGAGATA
TAGAAGTAAACTTGTGTCTCAAGAAGAAATTGAATTTGTCCATTGTGGAGATCCAGAA

Alignment

ORF - retro_pabe_735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.52 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMGSKM-ASASRVVQVVKPHTPLIRFPDRRDNPKPNVSEALRSAGLPSHSSVISQHSKGSKSPDLLM-YQ
          MM.SKM.ASASRV.QVVKPH.PLI.FP.RRDNPKPNV.EALRSAG.PSH.S.I...S..SK...LL....
Retrocopy MMSSKM<ASASRVIQVVKPHAPLISFPARRDNPKPNVPEALRSAG*PSHDSAI---SQHSKGSKLLD<FA

Parental  GPPDTAEIIKTLPQKYRRKLVSQEEIEFIQRGGPE
          ..PDTAE..KTLPQ.YR.KLVSQEEIEF...G.PE
Retrocopy DVPDTAEVMKTLPQRYRSKLVSQEEIEFVHCGDPE

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	0.06 RPM	7.52 RPM
SRP007412_cerebellum	0.00 RPM	6.57 RPM
SRP007412_heart	0.15 RPM	17.01 RPM
SRP007412_kidney	0.00 RPM	11.73 RPM
SRP007412_liver	0.31 RPM	6.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_735 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_735 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_823
Pan troglodytes	retro_ptro_573

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003161	2 retrocopies	retro_amel_1838, retro_amel_565,
Callithrix jacchus	ENSCJAG00000016092	2 retrocopies	retro_cjac_3202, retro_cjac_45,
Dipodomys ordii	ENSDORG00000007063	1 retrocopy	retro_dord_110,
Echinops telfairi	ENSETEG00000019493	2 retrocopies	retro_etel_1624, retro_etel_625,
Felis catus	ENSFCAG00000031782	1 retrocopy	retro_fcat_724,
Homo sapiens	ENSG00000134056	2 retrocopies	retro_hsap_2750, retro_hsap_823,
Loxodonta africana	ENSLAFG00000007932	2 retrocopies	retro_lafr_1243, retro_lafr_598,
Monodelphis domestica	ENSMODG00000019701	1 retrocopy	retro_mdom_1559,
Mus musculus	ENSMUSG00000061474	4 retrocopies	retro_mmus_105, retro_mmus_123, retro_mmus_3223, retro_mmus_753,
Nomascus leucogenys	ENSNLEG00000004071	4 retrocopies	retro_nleu_1545, retro_nleu_196, retro_nleu_2243, retro_nleu_257,
Oryctolagus cuniculus	ENSOCUG00000005261	2 retrocopies	retro_ocun_1057, retro_ocun_1109,
Otolemur garnettii	ENSOGAG00000024260	9 retrocopies	retro_ogar_1166, retro_ogar_1716, retro_ogar_2238, retro_ogar_2363, retro_ogar_2629, retro_ogar_3382, retro_ogar_711, retro_ogar_790, retro_ogar_869,
Ochotona princeps	ENSOPRG00000011392	1 retrocopy	retro_opri_587,
Pongo abelii	ENSPPYG00000015524	3 retrocopies	retro_pabe_2219, retro_pabe_735 , retro_pabe_917,
Pan troglodytes	ENSPTRG00000016944	4 retrocopies	retro_ptro_1858, retro_ptro_2038, retro_ptro_573, retro_ptro_690,
Pteropus vampyrus	ENSPVAG00000010843	1 retrocopy	retro_pvam_174,
Rattus norvegicus	ENSRNOG00000048862	2 retrocopies	retro_rnor_1792, retro_rnor_2014,
Ictidomys tridecemlineatus	ENSSTOG00000021863	2 retrocopies	retro_itri_1039, retro_itri_938,
Tupaia belangeri	ENSTBEG00000012048	22 retrocopies	retro_tbel_1313, retro_tbel_1494, retro_tbel_1527, retro_tbel_224, retro_tbel_2404, retro_tbel_2661, retro_tbel_2755, retro_tbel_2762, retro_tbel_2924, retro_tbel_2934, retro_tbel_3239, retro_tbel_3240, retro_tbel_359, retro_tbel_3891, retro_tbel_3893, retro_tbel_3941, retro_tbel_4124, retro_tbel_4429, retro_tbel_4515, retro_tbel_4543, retro_tbel_4592, retro_tbel_702,