RetrogeneDB ID: retro_pcap_434

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_86156:1476..1769(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTGES3
• Ensembl ID: ENSPCAG00000007779
• Aliases: None
• Description: prostaglandin E synthase 3 (cytosolic) [Source:HGNC Symbol;Acc:16049]

Sequence

>retro_pcap_434
GATCCAAATGATTCAAGAGTCAAAAAAAGGACAGATCAATCTCACATGTTTACACAAAGGAGAACCTGGCCAGTTGTGGC
CAAAGTTAACAAAAGAAAGAACAAAATTTCATTGGCTTAGTGTGAACTTCAATGATTGGAAAAACACACAAGATGATTCA
GATAAAGGCTTGCCTAGTTTTGACCATTTCTATTACCAATGTGGATAGTGATGAGGATGCAGATTTATTGGAAGTAGACA
GAGCAAACAGTAACTTGCAAGACAGTGATGATGAAGAAACGCCAGCTACAGAG

Alignment

ORF - retro_pcap_434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.92 %
• Parental protein coverage: 63.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DPDDS-KHKRTDRSI-LCCLRKGEPGQSWPRLTKERAKLNWLSVDFNNWKDWEDDSDEDMSNFDRFSEM-
          DP.DS.K....DRSI.L.CL.KGEPGQ.WP.LTKER.K..WLSV.FN...DW....D........F....
Retrocopy DPNDS<KSQKKDRSI<LTCLHKGEPGQLWPKLTKERTKFHWLSVNFN---DWKNTQDDSDKGLPSFDHF>

Parental  MNNMGGDEDVDLPEVDGADDDSQDSDDEKMPDLE
          ..N...DED.DL.EVD.A....QDSDDE..P..E
Retrocopy ITNVDSDEDADLLEVDRANSNLQDSDDEETPATE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_434 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,