RetrogeneDB ID: retro_pcap_412

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_75249:4531..4985(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BUB3
• Ensembl ID: ENSPCAG00000007736
• Aliases: None
• Description: BUB3 mitotic checkpoint protein [Source:HGNC Symbol;Acc:1151]

Sequence

>retro_pcap_412
GTATTGGTGTGGCACTTACAGAACATGGGCTACCTGCAGCAGTGCCAGGAATCCACCCTGAAAGCTAGACCCTTTGCATA
TGCACTTTCCAAACAAGCAAGGTTGTGGATTAGGCTCTGTTGACAGCTGGGTAGCCACCGAGTACTTGGACATAAGCCCT
GAGGTAAAAAAGAAGTATATCTTCGAATTTTAACAACTAAAATAAAATACTACGGAGATTTACCCAATAAATGACATTTC
CTTTCACAACATCCACAATGCATTTGCCACACGTGGTTCTGATGGCTTTGTAAATGTTTGGGATGCATCTAACAAAAAGT
GACTGTGCCAGTTTCAAAGATATCCTACCAGCATTGCATCCCTTGACTTCAGTAACAATGGAACTACCTGTGCGATAGCA
TCTTCATGTATGTATGAAATGGATGATGCAAAGCATCCTGATGATTGTATCTTT

Alignment

ORF - retro_pcap_412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.95 %
• Parental protein coverage: 64.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLVWDLRNMGYVQQRRESSLKYQ-TRCIRAF-PNKQGYVLSSIEGRVAVEYLDPSPEVQKKKYAFKCHRL
          VLVW.L.NMGY.QQ..ES.LK...T.CI..F.PNKQG..L.S....VA.EYLD.SPEV.KKKY.F....L
Retrocopy VLVWHLQNMGYLQQCQESTLKAR<TLCICTF<PNKQGCGLGSVDSWVATEYLDISPEV-KKKYIFEF*QL

Parental  KENNIEQIYPVNAISFHNIHNTFATGGSDGFVNIWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIASS
          K.N..E.IYP.N.ISFHNIHN.FAT.GSDGFVN.WD..NKK.LCQF.RYPTSIASL.FSN.GTT.AIASS
Retrocopy K*NTTE-IYPINDISFHNIHNAFATRGSDGFVNVWDASNKK*LCQFQRYPTSIASLDFSNNGTTCAIASS

Parental  YMYEMDDTEHPEDGVF
          .MYEMDD..HP.D..F
Retrocopy CMYEMDDAKHPDDCIF

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_412 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 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012700	1 retrocopy	retro_cfam_399,
Callithrix jacchus	ENSCJAG00000001066	1 retrocopy	retro_cjac_3085,
Cavia porcellus	ENSCPOG00000011957	1 retrocopy	retro_cpor_997,
Homo sapiens	ENSG00000154473	1 retrocopy	retro_hsap_3887,
Gorilla gorilla	ENSGGOG00000023971	1 retrocopy	retro_ggor_2614,
Myotis lucifugus	ENSMLUG00000017732	1 retrocopy	retro_mluc_627,
Macaca mulatta	ENSMMUG00000003092	1 retrocopy	retro_mmul_1729,
Nomascus leucogenys	ENSNLEG00000027075	1 retrocopy	retro_nleu_1887,
Procavia capensis	ENSPCAG00000007736	1 retrocopy	retro_pcap_412 ,
Pongo abelii	ENSPPYG00000002731	1 retrocopy	retro_pabe_3168,
Ictidomys tridecemlineatus	ENSSTOG00000021785	1 retrocopy	retro_itri_1095,
Tarsius syrichta	ENSTSYG00000013444	2 retrocopies	retro_tsyr_1652, retro_tsyr_732,
Tursiops truncatus	ENSTTRG00000016194	1 retrocopy	retro_ttru_1136,