RetrogeneDB ID: retro_pcap_146

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_112080:1039..1374(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL27
• Ensembl ID: ENSPCAG00000013249
• Aliases: None
• Description: ribosomal protein L27 [Source:HGNC Symbol;Acc:10328]

Sequence

>retro_pcap_146
TTATTGTGTAAGAACATTGATGGTGGCATTTCAGACCAGTCCTATAGCTATGCTCTGGGGACTGGAATTTACTGCTAACT
CTGCAAAGTAACAACTGCAGTGGGTAGGAATAAAGTTGTCAAGAGGTCAAAGATCAACTGTTTCATGAAAATGTAGAACT
GCAATCACCGACTAATGCCCACAGGGTACTTCTGTGGATATTCCTTTGGACAAAACTGCAGTAAACAAGAATGTCTTCAG
AGACCCTGCTCTTAAACACAAGTCTTAGCACGATGCCAAGGTCAAGTTTGAAGAGAGGTACAAGATGGCAAAACAAGTGG
TTCTTCCAGAAGCTG

Alignment

ORF - retro_pcap_146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 81.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRSKIKSFVKVYNYNH-LMPTRY-SVDIPL
          ...KNID.G.SD..YS.AL..GI.....KVT.A.G..K..KRSKI..F.K..N.NH.LMPT.Y.SVDIPL
Retrocopy LLCKNIDGGISDQSYSYALGTGIYC*LCKVTTAVGRNKVVKRSKINCFMKM*NCNHRLMPTGY>SVDIPL

Parental  DKTVVNKDVFRDPALKRKARREAKVKFEERYK-TGK-NKWFFQKL
          DKT.VNK.VFRDPALK.K....AKVKFEERYK..GK.NKWFFQKL
Retrocopy DKTAVNKNVFRDPALKHKS*HDAKVKFEERYK<DGK<NKWFFQKL

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_146 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 18 parental genes, and 106 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000200	3 retrocopies	retro_amel_122, retro_amel_37, retro_amel_674,
Bos taurus	ENSBTAG00000017441	6 retrocopies	retro_btau_1113, retro_btau_129, retro_btau_1565, retro_btau_1855, retro_btau_338, retro_btau_394,
Canis familiaris	ENSCAFG00000014630	6 retrocopies	retro_cfam_1193, retro_cfam_2109, retro_cfam_339, retro_cfam_364, retro_cfam_947, retro_cfam_959,
Callithrix jacchus	ENSCJAG00000013067	9 retrocopies	retro_cjac_1345, retro_cjac_1350, retro_cjac_1543, retro_cjac_1630, retro_cjac_2210, retro_cjac_275, retro_cjac_2828, retro_cjac_369, retro_cjac_776,
Echinops telfairi	ENSETEG00000002811	23 retrocopies	retro_etel_1230, retro_etel_1250, retro_etel_1302, retro_etel_1312, retro_etel_1453, retro_etel_1496, retro_etel_160, retro_etel_177, retro_etel_2055, retro_etel_2170, retro_etel_278, retro_etel_306, retro_etel_349, retro_etel_415, retro_etel_461, retro_etel_467, retro_etel_548, retro_etel_555, retro_etel_751, retro_etel_753, retro_etel_775, retro_etel_805, retro_etel_971,
Felis catus	ENSFCAG00000013142	6 retrocopies	retro_fcat_1026, retro_fcat_1184, retro_fcat_1824, retro_fcat_228, retro_fcat_698, retro_fcat_78,
Gorilla gorilla	ENSGGOG00000026039	6 retrocopies	retro_ggor_1741, retro_ggor_1852, retro_ggor_2546, retro_ggor_2630, retro_ggor_298, retro_ggor_907,
Loxodonta africana	ENSLAFG00000014220	3 retrocopies	retro_lafr_443, retro_lafr_739, retro_lafr_965,
Myotis lucifugus	ENSMLUG00000004119	1 retrocopy	retro_mluc_359,
Macaca mulatta	ENSMMUG00000008090	7 retrocopies	retro_mmul_1646, retro_mmul_1997, retro_mmul_418, retro_mmul_478, retro_mmul_52, retro_mmul_680, retro_mmul_925,
Monodelphis domestica	ENSMODG00000015128	1 retrocopy	retro_mdom_1141,
Mus musculus	ENSMUSG00000063316	2 retrocopies	retro_mmus_223, retro_mmus_277,
Nomascus leucogenys	ENSNLEG00000011901	2 retrocopies	retro_nleu_334, retro_nleu_45,
Oryctolagus cuniculus	ENSOCUG00000003872	1 retrocopy	retro_ocun_263,
Otolemur garnettii	ENSOGAG00000003940	14 retrocopies	retro_ogar_1091, retro_ogar_1297, retro_ogar_1478, retro_ogar_1692, retro_ogar_1887, retro_ogar_2189, retro_ogar_2354, retro_ogar_2625, retro_ogar_2687, retro_ogar_2915, retro_ogar_3207, retro_ogar_3294, retro_ogar_3381, retro_ogar_618,
Procavia capensis	ENSPCAG00000013249	4 retrocopies	retro_pcap_123, retro_pcap_146 , retro_pcap_203, retro_pcap_227,
Rattus norvegicus	ENSRNOG00000020674	8 retrocopies	retro_rnor_1150, retro_rnor_125, retro_rnor_1257, retro_rnor_1968, retro_rnor_2594, retro_rnor_2989, retro_rnor_386, retro_rnor_414,
Sarcophilus harrisii	ENSSHAG00000012042	4 retrocopies	retro_shar_10, retro_shar_253, retro_shar_730, retro_shar_741,