RetrogeneDB ID: retro_pcap_57

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_3149:112127..112897(+)
• Located in intron of: ENSPCAG00000015746

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS3A
• Ensembl ID: ENSPCAG00000015040
• Aliases: None
• Description: ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]

Sequence

>retro_pcap_57
GGCAAGGATAAATGCCTTACCAAGCTGGCAAAAAAGGAGTCAAGAAGAGAGTGGTTGATCCATTTTCTAAACAAGATCGG
AATGACGTAAAAGCACCACCTATGTGCAACATAAGGAATACTGGGAAAACACAGGTCACAAGAACTCAAGGAACAAAAAT
TGCATCTGATGGCCTCAAGGGTCATGTTTTTGAAGTCAGCCTTGCTGATCTGCAGAACAGTGAAGTTGCATTTAGAAAAT
TCAAGTTAATTACTGAGATGTTCAGGGCAAAAACTGTCTAATCAATTTCCATGGCATGGATCTTACCCGTGACAAAATGT
GCTCCATGGTCAAGAAACAGCAGACCATGACTGACGCTCATGCTGATGTCAAGGCTACAGATGGTTATTTGCTTTGTCCC
TTCTGTTTTGGTTTTACTGAAAAACGCAACAATCAGATTCAGAAGATGTCTTACGCTCAGCACCAACAGGTCCACCAAGT
CCAGAAGAAAAGGATGGAAATCATGACCCGAGAGGTGCAGACAAATGACTTGAAAGAAGTTGTCAACAAATTGATTCCAG
ACAGCATTGTGAAAGACATAGAAAAGGCTTGCCAATCTATTTATCCTCTCCATGGTGTGTTTGTTAGAAAAAGTGGAAAT
GCTGAAGAAGCCGAAGTTTGAACTGAGGAAACTCATGGAGCTTCACGGTGAAGGCAGTAGTTCTGGAAAAGCTACTGGAG
ATGAGACAGGTGCTAAAGTGGAACGAGCTGATGGCTATGAGCCAGCTGTT

Alignment

ORF - retro_pcap_57 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.38 %
• Parental protein coverage: 97.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GKNKRLTK-GGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLA
          GK.K.LTK..GKKG.KK.VVDPFSK.D..DVKAP.M.NIRN.GKT.VTRTQGTKIASDGLKG.VFEVSLA
Retrocopy GKDKCLTK<AGKKGVKKRVVDPFSKQDRNDVKAPPMCNIRNTGKTQVTRTQGTKIASDGLKGHVFEVSLA

Parental  DLQNDEVAFRKFKLITE-DVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVG
          DLQN.EVAFRKFKLITE.DVQGKNCL.NFHGMDLTRDKMCSMVKK.QTM..AH.DVK.TDGYLL..FC.G
Retrocopy DLQNSEVAFRKFKLITE<DVQGKNCLINFHGMDLTRDKMCSMVKKQQTMTDAHADVKATDGYLLCPFCFG

Parental  FTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVF
          FT.KRNNQI.K.SYAQHQQV.Q..KK.MEIMTREVQTNDLKEVVNKLIPDSI.KDIEKACQSIYPLH.VF
Retrocopy FTEKRNNQIQKMSYAQHQQVHQVQKKRMEIMTREVQTNDLKEVVNKLIPDSIVKDIEKACQSIYPLHGVF

Parental  VR-KVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVERADGYEPPV
          VR.KV.MLKKPKFEL.KLMELHGEGSSSGKATGDETGAKVERADGYEP.V
Retrocopy VR>KVEMLKKPKFELRKLMELHGEGSSSGKATGDETGAKVERADGYEPAV

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_57 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 14 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015569	9 retrocopies	retro_cpor_1154, retro_cpor_1229, retro_cpor_210, retro_cpor_383, retro_cpor_460, retro_cpor_555, retro_cpor_609, retro_cpor_646, retro_cpor_789,
Equus caballus	ENSECAG00000009573	6 retrocopies	retro_ecab_168, retro_ecab_222, retro_ecab_256, retro_ecab_597, retro_ecab_626, retro_ecab_885,
Felis catus	ENSFCAG00000031288	5 retrocopies	retro_fcat_1110, retro_fcat_134, retro_fcat_1878, retro_fcat_780, retro_fcat_858,
Loxodonta africana	ENSLAFG00000017660	3 retrocopies	retro_lafr_10, retro_lafr_38, retro_lafr_385,
Macaca mulatta	ENSMMUG00000021821	1 retrocopy	retro_mmul_2297,
Monodelphis domestica	ENSMODG00000000969	6 retrocopies	retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mustela putorius furo	ENSMPUG00000007139	8 retrocopies	retro_mputfur_1293, retro_mputfur_1363, retro_mputfur_278, retro_mputfur_316, retro_mputfur_504, retro_mputfur_695, retro_mputfur_764, retro_mputfur_847,
Mus musculus	ENSMUSG00000028081	2 retrocopies	retro_mmus_218, retro_mmus_254,
Procavia capensis	ENSPCAG00000015040	6 retrocopies	retro_pcap_211, retro_pcap_286, retro_pcap_355, retro_pcap_420, retro_pcap_456, retro_pcap_57 ,
Pongo abelii	ENSPPYG00000025869	27 retrocopies	retro_pabe_1339, retro_pabe_1572, retro_pabe_1636, retro_pabe_1895, retro_pabe_1899, retro_pabe_2117, retro_pabe_2570, retro_pabe_2578, retro_pabe_2661, retro_pabe_2769, retro_pabe_2779, retro_pabe_2826, retro_pabe_2942, retro_pabe_3014, retro_pabe_3076, retro_pabe_3186, retro_pabe_3214, retro_pabe_3560, retro_pabe_369, retro_pabe_3692, retro_pabe_394, retro_pabe_473, retro_pabe_550, retro_pabe_602, retro_pabe_789, retro_pabe_912, retro_pabe_985,
Pteropus vampyrus	ENSPVAG00000015406	24 retrocopies	retro_pvam_1053, retro_pvam_1056, retro_pvam_1058, retro_pvam_1138, retro_pvam_1180, retro_pvam_1203, retro_pvam_1476, retro_pvam_149, retro_pvam_311, retro_pvam_330, retro_pvam_354, retro_pvam_36, retro_pvam_368, retro_pvam_376, retro_pvam_462, retro_pvam_486, retro_pvam_582, retro_pvam_73, retro_pvam_754, retro_pvam_799, retro_pvam_86, retro_pvam_893, retro_pvam_917, retro_pvam_996,
Rattus norvegicus	ENSRNOG00000011893	1 retrocopy	retro_rnor_198,
Sarcophilus harrisii	ENSSHAG00000015088	2 retrocopies	retro_shar_777, retro_shar_95,
Ictidomys tridecemlineatus	ENSSTOG00000024203	1 retrocopy	retro_itri_58,