RetrogeneDB ID: retro_pcap_298

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_28434:12398..13085(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC3
• Ensembl ID: ENSPCAG00000010817
• Aliases: None
• Description: histone deacetylase 3 [Source:HGNC Symbol;Acc:4854]

Sequence

>retro_pcap_298
ATGGCCAAGACCGTGGCCTATCTCTAAGACCCGGACGTGGGCAACTTCCACTATGGGGCTGGACACCCTATGAAGCCCCA
TGGACTGGTGTTGACCCATAGCTTGGTTCTGCACTGTGGTATCTATAAGTTGATCGTCTGCAAGCCATACCAGGCTTCCC
AGCATGACACGTGCCGCTTCCACTCTGAGGACTACACTGACTTCCTGCAGAGAGTCAGCCCCACCAATATGCAAGGCTTC
ACCAAGAGCCTTAATGCCTTCAGTGTGGGTGATGACTGCCCAGTGTTTCCCGGGCTCTTTGAATTCTGCTCCTGTTACAC
AAGCTCCTCTCTGCAAGGAGCAACCCAACTGAACAAAACGATCCGTGGTATTGCCATTAACTGGGCTGGTGGCCAGCAGC
ATGCCAAGAAGTTTGAGGCTTCGGGCTTCTGCTATGTCAACAACATTGTAATTGAGATCCTGGAACTTCTCAAGTACCAC
CCTCGGGTTCTCTACCTTGATATTGACATCCACCATGGTGACGGGATTCAGGAAGCCTTCTACCTCACTGACCGAGTCAT
GACAGTGTCCTTCCACAAATATGGAAATTACTCCTTTCCTGGTACAGGTGACATGTGTGAAGTTGGAGTGGAGAATGGTC
ACTACCATTGTCTCAGCGTGCCCCTGAGGGATGGCATTGATGACCAG

Alignment

ORF - retro_pcap_298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.09 %
• Parental protein coverage: 53.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDYIDFL
          MAKTVAY..DPDVGNFHYGAGHPMKPH.L.LTHSLVLH.G.YK..IV.KPYQASQHD.CRFHSEDY.DFL
Retrocopy MAKTVAYL*DPDVGNFHYGAGHPMKPHGLVLTHSLVLHCGIYK-LIVCKPYQASQHDTCRFHSEDYTDFL

Parental  QRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIAINWAGGLHHAKKFE
          QRVSPTNMQGFTKSLNAF.VGDDCPVFPGLFEFCS.YT..SLQGATQLN..I..IAINWAGG..HAKKFE
Retrocopy QRVSPTNMQGFTKSLNAFSVGDDCPVFPGLFEFCSCYTSSSLQGATQLNKTIRGIAINWAGGQQHAKKFE

Parental  ASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYEVG
          ASGFCYVN.IVI.ILELLKYHPRVLY.DIDIHHGDG.QEAFYLTDRVMTVSFHKYGNY.FPGTGDM.EVG
Retrocopy ASGFCYVNNIVIEILELLKYHPRVLYLDIDIHHGDGIQEAFYLTDRVMTVSFHKYGNYSFPGTGDMCEVG

Parental  AESGRYYCLNVPLRDGIDDQ
          .E.G.Y.CL.VPLRDGIDDQ
Retrocopy VENGHYHCLSVPLRDGIDDQ

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_298 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008662	1 retrocopy	retro_mluc_642,
Macaca mulatta	ENSMMUG00000012588	1 retrocopy	retro_mmul_49,
Procavia capensis	ENSPCAG00000010817	1 retrocopy	retro_pcap_298 ,
Ictidomys tridecemlineatus	ENSSTOG00000016240	1 retrocopy	retro_itri_1661,
Tupaia belangeri	ENSTBEG00000007520	1 retrocopy	retro_tbel_1811,