RetrogeneDB ID: retro_pcap_166

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_128853:6540..7089(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSPCAG00000004904
• Aliases: None
• Description: chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]

Sequence

>retro_pcap_166
ATGGCCTCCAATAAAACTATATTGCAAACAATGGGAAGGAAGCAGAGTGGAAAGAGTAAAAAAGTTGAAGAAGTACAACC
TGAAGAATTTGTGGTAGAAAAAGTGCTGGACCGACGTGTAGTGAATGGAAAGGTGGAGTAATTCCTGAAGTGGAAGGGAT
TTACAGATGCTGACAATACTTGGGAACCTGAAGAAAATTTAGATTGTCCGGAATTAATTGAAGCGTTTCTCAAGTCTCAA
AAAGCTGGTAAAGAAAAAGATGGTACAGAAAGGAAGTCTTTATCTGACAGTGAATCTGATGACAGCAAATCAAAGAAGAA
AAGAGATGCTGCTCGCAAACCTAGAGGCTTTACAAGATGTCTTGATCCTGAACGAATAATTGGTGCCACAGACAGCAGTG
GAGAAGTAATGTTTCTCAGGAAATGGAAAGATGCAGATGAGGCTGACTTGGTGCTGGCAAAAGAGGCAAACATGAAGTGC
CCACAAATTGTAATTGCGTTTTATGAAGAGAGACTAACTTGGCATTCTTGTCCAGAAGATGAAGCTCAA

Alignment

ORF - retro_pcap_166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASNKTTLQKMGRKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCP
          MASNKT.LQ.MGRKQ.GKSKKVEE..PEEFVVEKVLDRRVVNGKVE.FLKWKGFTDADNTWEPEENLDCP
Retrocopy MASNKTILQTMGRKQSGKSKKVEEVQPEEFVVEKVLDRRVVNGKVE*FLKWKGFTDADNTWEPEENLDCP

Parental  ELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLM
          ELIEAFL.S............KSLSDSESDDSKSKKKRDAA.KPRGF.R.LDPERIIGATDSSGE.MFL.
Retrocopy ELIEAFLKSXXXXXXXXXXXXKSLSDSESDDSKSKKKRDAARKPRGFTRCLDPERIIGATDSSGEVMFLR

Parental  KWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ
          KWKD.DEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ
Retrocopy KWKDADEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ

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_166 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 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002897	11 retrocopies	retro_cfam_1157, retro_cfam_161, retro_cfam_1811, retro_cfam_1823, retro_cfam_1849, retro_cfam_2083, retro_cfam_502, retro_cfam_594, retro_cfam_739, retro_cfam_931, retro_cfam_948,
Callithrix jacchus	ENSCJAG00000007952	8 retrocopies	retro_cjac_1100, retro_cjac_1414, retro_cjac_1612, retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Equus caballus	ENSECAG00000012780	1 retrocopy	retro_ecab_784,
Loxodonta africana	ENSLAFG00000006907	3 retrocopies	retro_lafr_661, retro_lafr_687, retro_lafr_776,
Mus musculus	ENSMUSG00000029836	1 retrocopy	retro_mmus_77,
Otolemur garnettii	ENSOGAG00000016583	1 retrocopy	retro_ogar_136,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Procavia capensis	ENSPCAG00000002381	2 retrocopies	retro_pcap_134, retro_pcap_308,
Procavia capensis	ENSPCAG00000004904	2 retrocopies	retro_pcap_108, retro_pcap_166 ,
Rattus norvegicus	ENSRNOG00000011814	2 retrocopies	retro_rnor_120, retro_rnor_301,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,
Tarsius syrichta	ENSTSYG00000008159	6 retrocopies	retro_tsyr_1459, retro_tsyr_1545, retro_tsyr_1552, retro_tsyr_1645, retro_tsyr_203, retro_tsyr_583,
Tursiops truncatus	ENSTTRG00000000711	7 retrocopies	retro_ttru_1238, retro_ttru_1247, retro_ttru_1851, retro_ttru_294, retro_ttru_52, retro_ttru_591, retro_ttru_644,