RetrogeneDB ID: retro_pcap_323

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_36557:17608..18089(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN2A
• Ensembl ID: ENSPCAG00000011502
• Aliases: None
• Description: UBX domain protein 2A [Source:HGNC Symbol;Acc:27265]

Sequence

>retro_pcap_323
CTATCATTATAATTACAGGGGGGTTTTAGTAAAGAGGAGGTGGATGTTAAAGTTGAAGATAAGAAAAATGAAGTTTGTGT
GTCAACAAAACCTGTATTCCAGCCCTTCTCATGACAGGGGTCACAGACTAGAAAGTGCATACCAAAAATTGTTCCTAAAG
CAAAGAGTATTGAAGTTGAGAATGAAAACCATCCATGTACTATCCCATTAAACAACTTGGAACCCATCACTAACATACAG
ATCTGTCTAGCCAATGGGAAAAGGATTGTCCAGAAATTTAACATTTCTCATATCGTTAAACCACATCAAAGACTTCATTG
AAAAATACCAAGGATCTCAGAGCAGCTCTCCATTTTCTCTGGCAACAGCTCTTCCTTTCCTCATATTGCTGGATGAGACA
TTCACTGCAGGAGAAGCCAATTTACAGAATGCTATAATCATTCAGAAACTCCAGAGAGCATCTGAGCCCTTCAGAAGACT
T

Alignment

ORF - retro_pcap_323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.64 %
• Parental protein coverage: 65.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPLELQGAFNKEEVDVKVEDKKNEVCVSTKPVFQPFSGQGHRLGSATPKIVSKLKSTEVENENHPCTIPL
          L.L.LQG.F.KEEVDVKVEDKKNEVCVSTKPVFQPFS.QG.......PKIV.K.KS.EVENENHPCTIPL
Retrocopy LSL*LQGGFSKEEVDVKVEDKKNEVCVSTKPVFQPFS*QGSQTRKCIPKIVPKAKSIEVENENHPCTIPL

Parental  NNLEPITNIQIWLANGKRIVQKFNISHRV-SHIKDFIEKSQGSRRGPPFCLATALPFVRLLDETLTLAEA
          NNLEPITNIQI.LANGKRIVQKFNISH.V..HIKDFIEK.QGS....PF.LATALPF..LLDET.T..EA
Retrocopy NNLEPITNIQICLANGKRIVQKFNISHIV>NHIKDFIEKYQGSQSSSPFSLATALPFLILLDETFTAGEA

Parental  GLQNAVIIQRLQRAAEPFKGL
          .LQNA.IIQ.LQRA.EPF..L
Retrocopy NLQNAIIIQKLQRASEPFRRL

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_323 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 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001640	5 retrocopies	retro_chof_1096, retro_chof_1171, retro_chof_2641, retro_chof_961, retro_chof_964,
Callithrix jacchus	ENSCJAG00000007665	1 retrocopy	retro_cjac_2085,
Equus caballus	ENSECAG00000020144	1 retrocopy	retro_ecab_569,
Echinops telfairi	ENSETEG00000002623	1 retrocopy	retro_etel_1116,
Homo sapiens	ENSG00000173960	1 retrocopy	retro_hsap_2025,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463,
Myotis lucifugus	ENSMLUG00000015640	1 retrocopy	retro_mluc_1195,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909,
Procavia capensis	ENSPCAG00000011502	4 retrocopies	retro_pcap_169, retro_pcap_255, retro_pcap_271, retro_pcap_323 ,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Rattus norvegicus	ENSRNOG00000004950	2 retrocopies	retro_rnor_1746, retro_rnor_2966,
Sorex araneus	ENSSARG00000010108	1 retrocopy	retro_sara_272,
Sus scrofa	ENSSSCG00000026283	1 retrocopy	retro_sscr_537,
Tupaia belangeri	ENSTBEG00000012158	1 retrocopy	retro_tbel_3887,