RetrogeneDB ID: retro_pcap_272

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_2485:56311..57125(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000011171
• Aliases: None
• Description: None

Sequence

>retro_pcap_272
GTTTGGTCCCTACCCAGGGTCCTCTGCAGTGCATGAAGCGAGATGTTGAGGCAGAGCTTGGAAAGCCAAGACGCTCAAAC
CAGACAACTGTAAAATCCTGTCACAAGTATGGAGAAGCATTATGGAGGGGTGTGTCAAAATTTTGCTGCTCATCTGAGGA
AAGCTACCAGACTGTAATACAAAGAAAGTCTCCTGGTGAATGAAATCAGATTGTGTGCCTCTACAGGGACCCCACACTTA
AAGCAAGGCCTGAAAACTTTGCCAATGAGTTTGCTAAACTTCAGGATTATTGATAAGCAATGGTTGAAAGATTTGAAGTT
AAAGTAGTTAAATCTCTTAAAGTCTATCAAACAGTTGTAAAAATTAAGTGGATGATCTCAAAGCAACATTATCAAGGAAT
CAAGAAGACAAGCAGTTAATCCAGTTGCAGAGGGCATGTCATTGAAACCCATCTGATCAATATGTTATTTCATAGGCAGA
AATGGAATTACAGGGAGCTGCAATGGATACTACCTGAACAATCGGTCACCAGGAGGAAACTATGACAACTTTGAAAATCA
GAAGATAAAGGAAATAAAGAACATATTTTCAGAAGTTATCTCTTTTGAAATGTTATTTTACTGCAAAGCTGTAGAGGTCT
ATACTGCTGCCTACCAAAAATATACAAAACATTGATGAGGAAGAAGATTTAGAGATTGTCTGAAACTCTCTGTATCCACC
AGATCTTTCATCTCATTTATATATCGTAAGAACAAATTCAAAGTCACCTGTTAAGAGATTGCTGTCAACTAAGCGTGTAT
CTAGAAAAGGGCAG

Alignment

ORF - retro_pcap_272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.26 %
• Parental protein coverage: 84.78 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VGSRSGVVCRARGRMLRRSLESRDAQTRQLQDAVTNVEKHFGELCQIFAAYVRKTARLRDKADLLVNEIN
          V.S...V.C.A...MLR.SLES.DAQTRQL...VT..EKH.G..CQ.FAA..RK..RL..K..LLVNEI.
Retrocopy VWSLPRVLCSA*SEMLRQSLESQDAQTRQL*NPVTSMEKHYGGVCQNFAAHLRKATRL*YKESLLVNEIR

Parental  MYASTETPNLKQGLK-NFADEFAKLQDYRQAEVERLEAKVVEPLKAYGTIVKMKR-DDLKATLTARNREA
          ..AST.TP.LKQGLK.NFA.EFAKLQDY..A.VER.E.KVV..LK.Y.T.VK.K..DDLKATL..RN.E.
Retrocopy LCASTGTPHLKQGLK<NFANEFAKLQDY**AMVERFEVKVVKSLKVYQTVVKIKW<DDLKATLS-RNQED

Parental  KQLTQLERTRQRNPSDRHVISQAETELQRATMDATRTTRHLEETI-DHFEKQKIKDIKNVFSEFITIEML
          KQL.QL.R....NPSD..VIS.AE.ELQ.A.MD.T.T..H.EET..D.FE.QKIK.IKN.FSE.I..EML
Retrocopy KQLIQLQRACH*NPSDQYVIS*AEMELQGAAMDTT*TIGHQEETM<DNFENQKIKEIKNIFSEVISFEML

Parental  FHGKALEVYTAAYQ-NIQKIDEEEDLEVFRNTLYPQDYSSRLDIVRANSKSPLQRSLSAKCVSGTGQ
          F..KA.EVYTAAYQ.NIQ.IDEEEDLE...N.LYP.D.SS.L.IVR.NSKSP..R.LS.K.VS..GQ
Retrocopy FYCKAVEVYTAAYQ>NIQNIDEEEDLEIV*NSLYPPDLSSHLYIVRTNSKSPVKRLLSTKRVSRKGQ

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_272 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 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009105	1 retrocopy	retro_cfam_1072,
Echinops telfairi	ENSETEG00000013003	1 retrocopy	retro_etel_522,
Homo sapiens	ENSG00000188343	1 retrocopy	retro_hsap_1485,
Gorilla gorilla	ENSGGOG00000006452	1 retrocopy	retro_ggor_1137,
Loxodonta africana	ENSLAFG00000003954	1 retrocopy	retro_lafr_201,
Microcebus murinus	ENSMICG00000006797	1 retrocopy	retro_mmur_415,
Monodelphis domestica	ENSMODG00000007447	2 retrocopies	retro_mdom_1239, retro_mdom_827,
Mustela putorius furo	ENSMPUG00000009112	1 retrocopy	retro_mputfur_1183,
Nomascus leucogenys	ENSNLEG00000002773	1 retrocopy	retro_nleu_1707,
Otolemur garnettii	ENSOGAG00000002972	1 retrocopy	retro_ogar_654,
Oreochromis niloticus	ENSONIG00000002446	1 retrocopy	retro_onil_57,
Procavia capensis	ENSPCAG00000011171	1 retrocopy	retro_pcap_272 ,
Pongo abelii	ENSPPYG00000018744	2 retrocopies	retro_pabe_1235, retro_pabe_2497,
Tarsius syrichta	ENSTSYG00000012502	1 retrocopy	retro_tsyr_975,
Tursiops truncatus	ENSTTRG00000012378	1 retrocopy	retro_ttru_45,