RetrogeneDB ID: retro_pcap_330

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_38489:11863..12136(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPE1
• Ensembl ID: ENSPCAG00000009541
• Aliases: None
• Description: heat shock 10kDa protein 1 (chaperonin 10) [Source:HGNC Symbol;Acc:5269]

Sequence

>retro_pcap_330
CTCTTTGACCGCATATTGGTGGAAAGCATTGCAGCTGAAACGGTAACTAAAGGAAGCTTTATGCTTCCAGAAAAATCTCA
AGGAAAAGTACTTCAAGCAGCAGTAGTGGCTATTGGTTCCGGATCTAAATGAAAGGGTGGAGAGATTCAACCAGTTAGCG
TGAAAGTTGGTAATAAAGTTCTTCTCCCCGAATGTGGAGGCACCAAAGTAGTTCTGGGATGACAAGGATTATTTCTATTT
AGAGATGGTGACATTCTTGGGAAGTATGTAGAC

Alignment

ORF - retro_pcap_330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.1 %
• Parental protein coverage: 89.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDKVLLPEYGGTKV
          LFDR.LVE..AAETVTKG..MLPEKSQGKVLQA.VVA.GSGSK.KGGEIQPVSVKVG.KVLLPE.GGTKV
Retrocopy LFDRILVESIAAETVTKGSFMLPEKSQGKVLQAAVVAIGSGSK*KGGEIQPVSVKVGNKVLLPECGGTKV

Parental  VL-DDKDY-FLFRDGDILGKYVD
          VL.DDKDY.FLFRDGDILGKYVD
Retrocopy VL>DDKDY<FLFRDGDILGKYVD

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_330 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 6 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004008	1 retrocopy	retro_cjac_254,
Dasypus novemcinctus	ENSDNOG00000013246	27 retrocopies	retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Homo sapiens	ENSG00000115541	18 retrocopies	retro_hsap_1066, retro_hsap_1152, retro_hsap_1351, retro_hsap_1524, retro_hsap_1646, retro_hsap_1703, retro_hsap_2248, retro_hsap_2402, retro_hsap_2480, retro_hsap_2812, retro_hsap_2813, retro_hsap_3455, retro_hsap_3540, retro_hsap_366, retro_hsap_3664, retro_hsap_4194, retro_hsap_495, retro_hsap_963,
Gorilla gorilla	ENSGGOG00000027944	17 retrocopies	retro_ggor_1051, retro_ggor_117, retro_ggor_1243, retro_ggor_1545, retro_ggor_157, retro_ggor_1676, retro_ggor_1821, retro_ggor_1956, retro_ggor_1957, retro_ggor_1958, retro_ggor_2331, retro_ggor_2391, retro_ggor_2476, retro_ggor_2492, retro_ggor_775, retro_ggor_841, retro_ggor_897,
Procavia capensis	ENSPCAG00000009541	1 retrocopy	retro_pcap_330 ,
Sus scrofa	ENSSSCG00000016078	7 retrocopies	retro_sscr_103, retro_sscr_1059, retro_sscr_106, retro_sscr_1088, retro_sscr_294, retro_sscr_298, retro_sscr_401,