RetrogeneDB ID: retro_pcap_135

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_100638:5913..6214(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL12
• Ensembl ID: ENSPCAG00000007469
• Aliases: None
• Description: ribosomal protein L12 [Source:HGNC Symbol;Acc:10302]

Sequence

>retro_pcap_135
AAATGCACCATTTAGAACAAAAATGTCCTGAATGAAGGTGGTACATTCTGCTCTGTCATAATCATCATGGTCGTCAAGAA
ACCACCCAGAGAAAGAAAGAACAGAAAAATATTAAGCACAGTGGAAATATCACTTTTGCTTAAATTCACAAGGCTGCCCA
ACAAACTACCACACCAATCTTTAGCCGGGGAACTCTCTGGAACTCTTAAGGGGGTCTTTGGGGACTGCGTGGTCTGTGGG
CTGCAATGCTGATGGTCACCACACTCATGACATCAGTGGTGGTGTGGAGGAAGGCCCAGTT

Alignment

ORF - retro_pcap_135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.37 %
• Parental protein coverage: 65.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLTIQNRQAQIEVVPSASALIIKALKEPPRDRK-KQKNIKHSGNITFDEIVGIARQ-MRHRSLARELSGT
          K.TI.N.....E.....S..II...K.PPR.RK..QKNIKHSGNITF..I...A.Q...H.SLA.ELSGT
Retrocopy KCTI*NKNVLNEGGTFCSVIIIMVVKKPPRERK<EQKNIKHSGNITFA*IHKAAQQ>LPHQSLAGELSGT

Parental  IKEI-LGTAQSVGCNVDGRHPHDIIDDINSGAV
          .K...LGTA.SVGCN.DG.H.HDI......G.V
Retrocopy LKGV>LGTAWSVGCNADGHHTHDISGGVEEGPV

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_135 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 8 parental genes, and 104 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008412	48 retrocopies	retro_dnov_1021, retro_dnov_1039, retro_dnov_1105, retro_dnov_1111, retro_dnov_1291, retro_dnov_1292, retro_dnov_1339, retro_dnov_1355, retro_dnov_1383, retro_dnov_1387, retro_dnov_1408, retro_dnov_1636, retro_dnov_1658, retro_dnov_1695, retro_dnov_1711, retro_dnov_1884, retro_dnov_2053, retro_dnov_2055, retro_dnov_2058, retro_dnov_210, retro_dnov_2165, retro_dnov_2196, retro_dnov_2199, retro_dnov_2222, retro_dnov_231, retro_dnov_2370, retro_dnov_2430, retro_dnov_2452, retro_dnov_2485, retro_dnov_2490, retro_dnov_260, retro_dnov_2603, retro_dnov_2637, retro_dnov_2639, retro_dnov_330, retro_dnov_343, retro_dnov_368, retro_dnov_387, retro_dnov_395, retro_dnov_455, retro_dnov_552, retro_dnov_560, retro_dnov_590, retro_dnov_597, retro_dnov_614, retro_dnov_634, retro_dnov_654, retro_dnov_677,
Latimeria chalumnae	ENSLACG00000015373	3 retrocopies	retro_lcha_31, retro_lcha_87, retro_lcha_92,
Loxodonta africana	ENSLAFG00000017669	10 retrocopies	retro_lafr_1, retro_lafr_193, retro_lafr_204, retro_lafr_286, retro_lafr_342, retro_lafr_41, retro_lafr_8, retro_lafr_802, retro_lafr_830, retro_lafr_984,
Macropus eugenii	ENSMEUG00000007380	12 retrocopies	retro_meug_1102, retro_meug_1107, retro_meug_1199, retro_meug_1357, retro_meug_1426, retro_meug_1611, retro_meug_1634, retro_meug_1691, retro_meug_1953, retro_meug_265, retro_meug_479, retro_meug_493,
Monodelphis domestica	ENSMODG00000004571	9 retrocopies	retro_mdom_1061, retro_mdom_1177, retro_mdom_1192, retro_mdom_1526, retro_mdom_1719, retro_mdom_1871, retro_mdom_1947, retro_mdom_309, retro_mdom_925,
Procavia capensis	ENSPCAG00000007469	3 retrocopies	retro_pcap_135 , retro_pcap_253, retro_pcap_306,
Rattus norvegicus	ENSRNOG00000016220	4 retrocopies	retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,
Tursiops truncatus	ENSTTRG00000015700	15 retrocopies	retro_ttru_1215, retro_ttru_1328, retro_ttru_1356, retro_ttru_1373, retro_ttru_1390, retro_ttru_1449, retro_ttru_1685, retro_ttru_1847, retro_ttru_187, retro_ttru_1942, retro_ttru_342, retro_ttru_421, retro_ttru_536, retro_ttru_65, retro_ttru_774,