RetrogeneDB ID: retro_pcap_222

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_184814:660..1112(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2A
• Ensembl ID: ENSPCAG00000005045
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2A [Source:HGNC Symbol;Acc:12472]

Sequence

>retro_pcap_222
ATGTTGACACCAGCCAGAAGGAGGCTTATGTGAGATTTCAAGGGGTTGCAAGAGGGCCCACCTGTGGGTGTTAGTGGCGC
CCCATCTGAAAACAACATCATGCAGTGGAATGCCATTAGATTTGGACCAGAAGGGACACACTTTGAAGATGGTACTCTGA
AACTAGGAATAGAATTTTCTGAAGAATGTCCAAATAAACTACCAACCGTTAGGTTTTTATCCAGAATGTTTCACCCAAAT
ACATACGCTGATGGTGGCACATGTTTAGCTACCCTTCGGAACCGATGGAGTCCAACATACGACATTTCTTCTGTCTTAAT
GTCGATTCAGTTTCTGCTGGATGAACCAAGTCCAAATAGCCCAGCTGCCAGCCAGCAGCACAACTTTATCAGGAAAATAA
GCAAGAAGACGAGAGAAGAGTTTCTGCCGTTGTTGAACAAAGCTGGAACGAT

Alignment

ORF - retro_pcap_222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.71 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTPARRRLMRDFKRLQEDPPAGVSGAPSENNIMVWNAVIFGXXXXXXXXXTFKLTIEFTEEYPNKPRTV
          M.TPARRRLM.DFK.LQE.PP.GVSGAPSENNIM.WNA..FG.........T.KL.IEF.EE.PNK..TV
Retrocopy MLTPARRRLM*DFKGLQEGPPVGVSGAPSENNIMQWNAIRFGPEGTHFEDGTLKLGIEFSEECPNKLPTV

Parental  RFVSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQ-AAQLYQENKREYEK
          RF.S.MFHPN.YADG..CL..L.NRWSPTYD.SS.L.SIQ.LLDEP.PNSPA.SQ.AAQLYQENK.E.E.
Retrocopy RFLSRMFHPNTYADGGTCLATLRNRWSPTYDISSVLMSIQFLLDEPSPNSPAASQ<AAQLYQENKQEDER

Parental  RVSAIVEQSWRD
          RVSA.VEQSW.D
Retrocopy RVSAVVEQSWND

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_222 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001079	1 retrocopy	retro_chof_1316,
Callithrix jacchus	ENSCJAG00000005098	2 retrocopies	retro_cjac_1180, retro_cjac_3862,
Cavia porcellus	ENSCPOG00000011908	1 retrocopy	retro_cpor_489,
Dasypus novemcinctus	ENSDNOG00000007060	1 retrocopy	retro_dnov_215,
Macropus eugenii	ENSMEUG00000003026	1 retrocopy	retro_meug_2180,
Monodelphis domestica	ENSMODG00000010209	1 retrocopy	retro_mdom_341,
Oryctolagus cuniculus	ENSOCUG00000016739	1 retrocopy	retro_ocun_183,
Otolemur garnettii	ENSOGAG00000024335	1 retrocopy	retro_ogar_3203,
Procavia capensis	ENSPCAG00000005045	1 retrocopy	retro_pcap_222 ,
Sus scrofa	ENSSSCG00000012621	1 retrocopy	retro_sscr_29,
Tarsius syrichta	ENSTSYG00000000888	1 retrocopy	retro_tsyr_676,