RetrogeneDB ID: retro_pcap_339

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_42138:14073..15023(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP0
• Ensembl ID: ENSPCAG00000016429
• Aliases: None
• Description: ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]

Sequence

>retro_pcap_339
ATGCCCAGGGAAGACAGGGCAACTTGGAAGTCCAACTACTTCCTTAAGATCATCCAACTTTTGGATGATTATCCCAAATG
CTTCATTGTGGGAGCAGACAATGTGGGCTCCAAGCAGATGCAGCAGATCCGCATGTCCCTCCGTGGGAAAGCCGTGGTCC
TGATGGGCAAGAACACCATGATGCGCAAGGCCATCCGAGGACACCTGGAAAACAACCCAGCTCTGGAGAAACTGTTGCCT
CACATCCGAGGTAATGTGGGCTTTGTGTTCACTAAGGAGGACCTTACAGAGATCAGGGACATGCTACTGGCTAACAAGGT
GCCAGCTGCTGCCCATGCTGGTGCCATTGCCCCATGTGAGGTTACTGTGCCAGCACAGAACACTGGTCTGTGTCCCCAGA
AGACTTCCTTCTTCCAGGCTTTGGGCATCACCACGAAGATCTCCAGAGGCACCATTGAAATCCTGAGTGATGTGCAGCTG
ATTAAAACTGGAGACAAAGTGGGAGCCAGCGAAGCCACCCTGCTGAACATGCTGAACATCTCCCCGTTCTCCTTCGGGCT
GGTCATCCAGCAGGTGTTTGACAGTGGCAGCATCTACAACCCGGAAGTGCTTGACATCACCAAGGATACTTTGCGTTCTC
GCTTCCTGGAGGGTGTCCGAAATGTTGCCGGCGTATGTCTGCAGATCGGTTACCCAACTGTTGCCTCAGTACCCCACTCT
ATCATCAATGGGTACAAGCGGGTTCTGGCTTTGTCTGTGGAGACCGATTACACCTTTCCACTGGCTGAAAAGGTTAAGGC
CTTCTTGGCTGATCCATCTGCATTTGTGGTTGCTGCCCTGTGGCCACCGCCTCTGCTGCTGCTGCTGCTGCTGCTTTGGC
CCCAGCCAAAGTTGAAGCCAAGGAAGAGTCGGAGGGGTCGGATGAAGATATGGGATTTGGTCTCTTTGAC

Alignment

ORF - retro_pcap_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLE
          MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLE
Retrocopy MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLE

Parental  NNPALEKLLLHIRGNV-FVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQA
          NNPALEKLL.HIRGNV.FVFTKEDLTEIRDMLLANKVPAAA.AGAIAPCEVTVPAQNTGL.P.KTSFFQA
Retrocopy NNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAAHAGAIAPCEVTVPAQNTGLCPQKTSFFQA

Parental  LGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLDITEDT
          LGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFD.GSIYNPEVLDIT.DT
Retrocopy LGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDSGSIYNPEVLDITKDT

Parental  LHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADPSAFVAAA-
          L.SRFLEGVRNVA.VCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADPSAFV.AA.
Retrocopy LRSRFLEGVRNVAGVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADPSAFVVAA<

Parental  PVAAAAAAAPAAASAPAKVEAKEESEESDEDMGFGLFD
          PVA.A.........APAKVEAKEESE.SDEDMGFGLFD
Retrocopy PVATAXXXXXXXXLAPAKVEAKEESEGSDEDMGFGLFD

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_339 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 20 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005144	4 retrocopies	retro_amel_1179, retro_amel_1194, retro_amel_1377, retro_amel_847,
Canis familiaris	ENSCAFG00000010227	5 retrocopies	retro_cfam_1580, retro_cfam_224, retro_cfam_487, retro_cfam_534, retro_cfam_693,
Choloepus hoffmanni	ENSCHOG00000002745	2 retrocopies	retro_chof_1115, retro_chof_2341,
Callithrix jacchus	ENSCJAG00000008677	3 retrocopies	retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus	ENSCPOG00000021812	5 retrocopies	retro_cpor_298, retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Equus caballus	ENSECAG00000015816	2 retrocopies	retro_ecab_1090, retro_ecab_585,
Felis catus	ENSFCAG00000013354	1 retrocopy	retro_fcat_441,
Homo sapiens	ENSG00000089157	7 retrocopies	retro_hsap_1403, retro_hsap_1553, retro_hsap_1889, retro_hsap_2095, retro_hsap_2334, retro_hsap_512, retro_hsap_784,
Gorilla gorilla	ENSGGOG00000026582	5 retrocopies	retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Myotis lucifugus	ENSMLUG00000001970	11 retrocopies	retro_mluc_1016, retro_mluc_1460, retro_mluc_1503, retro_mluc_1806, retro_mluc_1966, retro_mluc_2293, retro_mluc_268, retro_mluc_497, retro_mluc_564, retro_mluc_565, retro_mluc_882,
Macaca mulatta	ENSMMUG00000009157	2 retrocopies	retro_mmul_2245, retro_mmul_939,
Mus musculus	ENSMUSG00000067274	2 retrocopies	retro_mmus_143, retro_mmus_2249,
Oryctolagus cuniculus	ENSOCUG00000005749	2 retrocopies	retro_ocun_293, retro_ocun_376,
Otolemur garnettii	ENSOGAG00000003843	4 retrocopies	retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Procavia capensis	ENSPCAG00000016429	6 retrocopies	retro_pcap_232, retro_pcap_314, retro_pcap_339 , retro_pcap_353, retro_pcap_408, retro_pcap_67,
Petromyzon marinus	ENSPMAG00000001339	1 retrocopy	retro_pmar_6,
Pongo abelii	ENSPPYG00000005022	5 retrocopies	retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Rattus norvegicus	ENSRNOG00000001148	3 retrocopies	retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii	ENSSHAG00000001623	2 retrocopies	retro_shar_286, retro_shar_413,
Tursiops truncatus	ENSTTRG00000005658	1 retrocopy	retro_ttru_965,