RetrogeneDB ID: retro_mmul_1988

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:161887208..161887686(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000010233
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.4022
• Ensembl ID: ENSMMUG00000013766
• Aliases: None
• Description: prostaglandin E synthase 3 [Source:RefSeq peptide;Acc:NP_001248443]

Sequence

>retro_mmul_1988
ATGCAGCCTGCTTCTGCAAAGTGGTGCGATCGAAGGGACTATGTCTTCATTGAATTTTGTGTTGAAGATATAAGGATGTT
AATGTAAATTTTGAAAAATCCAACCTTACATTCAGTTGTCTTGGAGAAAGTGATAATTTTAAGCACTTAAATGAAATTGA
TCTTTTTTACTGTATTGATCCAAATGATTCCAAGCATAAAAGAATGGACAGATCAATTTTGTATTGTTTACAAACAGGAG
AATCTGGCCAGTCATGGCCAAAGTTAACAAAAGAAAGGGCAAAGCTGAATTGTCTTAGTGTGGACTTGAATAATTGGAAA
GACTGGGAAGATGGTTCAGATGAAGACAGGTCTAATTTTGATAGTTTCTCCGAGATGATGAACAACATGGGTGGTGATGA
GGATGTAGATTTACCAGAAGTAGATGAAGCAAATGATGATTCACAAGACAGTGATGATGAAAAATGCCAGATCTGGAG

Alignment

ORF - retro_mmul_1988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.27 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQPASAKWYDRRDYVFIEFCVEDS-KDVNVNFEKSKLTFSCLGGSDNFKHLNEIDLFHCIDPNDSKHKRT
          MQPASAKW.DRRDYVFIEFCVED..KDVNVNFEKS.LTFSCLG.SDNFKHLNEIDLF.CIDPNDSKHKR.
Retrocopy MQPASAKWCDRRDYVFIEFCVEDI<KDVNVNFEKSNLTFSCLGESDNFKHLNEIDLFYCIDPNDSKHKRM

Parental  DRSILCCLRKGESGQSWPRLTKERAKLNWLSVDFNNWKDWEDDSDEDMSNFDRFSEMMNNMGGDEDVDLP
          DRSIL.CL..GESGQSWP.LTKERAKLN.LSVD.NNWKDWED.SDED.SNFD.FSEMMNNMGGDEDVDLP
Retrocopy DRSILYCLQTGESGQSWPKLTKERAKLNCLSVDLNNWKDWEDGSDEDRSNFDSFSEMMNNMGGDEDVDLP

Parental  EVDGADDDSQDSDDE-KMPDLE
          EVD.A.DDSQDSDDE.KMPDLE
Retrocopy EVDEANDDSQDSDDE<KMPDLE

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	0.11 RPM	96.14 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	69.89 RPM
SRP007412_cerebellum	0.00 RPM	103.38 RPM
SRP007412_heart	0.00 RPM	56.65 RPM
SRP007412_kidney	0.00 RPM	73.36 RPM
SRP007412_liver	0.00 RPM	52.65 RPM
SRP007412_testis	0.04 RPM	99.66 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1988 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1988 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004172	1 retrocopy	retro_amel_1835,
Bos taurus	ENSBTAG00000017967	2 retrocopies	retro_btau_1766, retro_btau_275,
Choloepus hoffmanni	ENSCHOG00000006514	1 retrocopy	retro_chof_1336,
Callithrix jacchus	ENSCJAG00000010724	6 retrocopies	retro_cjac_1001, retro_cjac_1304, retro_cjac_2122, retro_cjac_3826, retro_cjac_473, retro_cjac_942,
Cavia porcellus	ENSCPOG00000000057	2 retrocopies	retro_cpor_183, retro_cpor_523,
Dasypus novemcinctus	ENSDNOG00000011310	4 retrocopies	retro_dnov_2088, retro_dnov_2571, retro_dnov_472, retro_dnov_969,
Dipodomys ordii	ENSDORG00000000964	2 retrocopies	retro_dord_600, retro_dord_94,
Echinops telfairi	ENSETEG00000000024	1 retrocopy	retro_etel_1612,
Homo sapiens	ENSG00000110958	5 retrocopies	retro_hsap_2084, retro_hsap_3122, retro_hsap_417, retro_hsap_618, retro_hsap_623,
Gorilla gorilla	ENSGGOG00000027957	5 retrocopies	retro_ggor_111, retro_ggor_135, retro_ggor_154, retro_ggor_542, retro_ggor_546,
Loxodonta africana	ENSLAFG00000008268	1 retrocopy	retro_lafr_490,
Macropus eugenii	ENSMEUG00000001288	1 retrocopy	retro_meug_264,
Myotis lucifugus	ENSMLUG00000015927	3 retrocopies	retro_mluc_1111, retro_mluc_2120, retro_mluc_836,
Macaca mulatta	ENSMMUG00000013766	6 retrocopies	retro_mmul_1054, retro_mmul_1988 , retro_mmul_2239, retro_mmul_2421, retro_mmul_679, retro_mmul_978,
Mus musculus	ENSMUSG00000071072	2 retrocopies	retro_mmus_2441, retro_mmus_2757,
Nomascus leucogenys	ENSNLEG00000017454	3 retrocopies	retro_nleu_2133, retro_nleu_2486, retro_nleu_446,
Otolemur garnettii	ENSOGAG00000028667	3 retrocopies	retro_ogar_1035, retro_ogar_1748, retro_ogar_2858,
Procavia capensis	ENSPCAG00000007779	2 retrocopies	retro_pcap_29, retro_pcap_434,
Pongo abelii	ENSPPYG00000004669	4 retrocopies	retro_pabe_2010, retro_pabe_2579, retro_pabe_5, retro_pabe_553,
Pan troglodytes	ENSPTRG00000005108	8 retrocopies	retro_ptro_1533, retro_ptro_1945, retro_ptro_2111, retro_ptro_2926, retro_ptro_319, retro_ptro_452, retro_ptro_454, retro_ptro_609,
Rattus norvegicus	ENSRNOG00000002642	5 retrocopies	retro_rnor_1011, retro_rnor_119, retro_rnor_1836, retro_rnor_1931, retro_rnor_2895,
Sorex araneus	ENSSARG00000007751	2 retrocopies	retro_sara_489, retro_sara_507,
Tupaia belangeri	ENSTBEG00000002994	15 retrocopies	retro_tbel_1658, retro_tbel_2266, retro_tbel_2370, retro_tbel_2383, retro_tbel_2598, retro_tbel_2622, retro_tbel_2823, retro_tbel_3798, retro_tbel_402, retro_tbel_407, retro_tbel_4279, retro_tbel_4432, retro_tbel_4461, retro_tbel_450, retro_tbel_997,
Tarsius syrichta	ENSTSYG00000009622	2 retrocopies	retro_tsyr_1264, retro_tsyr_177,