RetrogeneDB ID: retro_pcap_138

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_102639:9500..9864(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V2
• Ensembl ID: ENSPCAG00000000293
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 variant 2 [Source:HGNC Symbol;Acc:12495]

Sequence

>retro_pcap_138
AAAGGAGTAGGTGATGGCAGGCTTAGTTGGGCCTTGAAGATGATAAAGACATGGAACTTAGAAGATAGATAGGTGTGTTT
ATTGGGCCACCAAGAACAAATTATGAAAACAAAATAGATAGCCTGAAAGTAGAATATGGATCTAAATACTCAGAAGTTTC
TCCATCGGTTAGATTTGTAACAAAAATTAATATGAAAGGAATAAATAATCCCAGTGGAGTAGTGGAAGCACAGATGGTAC
TAGCATTAGCAAAATGCAAAATTCATACAACATTAAAGTTGTACTTCGAGAGCTAAGATGTCTAATGACGACCAACGAAA
ATATGAAACTTCCAAAGCCACTGGAAAGACAAATGTTCAACACT

Alignment

ORF - retro_pcap_138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.26 %
• Parental protein coverage: 84.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGVGDGTVSW-GLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEVPPSVRFVTKINMNGIN
          KGVGDG..SW.GLEDD.DM.L.R..G..IGPPRTNYEN.I.SLKVE.G.KY.EV.PSVRFVTKINM.GIN
Retrocopy KGVGDGRLSW<GLEDDKDMELRR*IGVFIGPPRTNYENKIDSLKVEYGSKYSEVSPSVRFVTKINMKGIN

Parental  NSSGVVEAQMVLA-LAK-QNSYNIKVVLRELRCLMTTNENMKLPKPLERQMFNT
          N.SGVVEAQMVLA...K.QNSYNIKVVLRELRCLMTTNENMKLPKPLERQMFNT
Retrocopy NPSGVVEAQMVLA<ISKMQNSYNIKVVLRELRCLMTTNENMKLPKPLERQMFNT

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_138 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032182	1 retrocopy	retro_cjac_814,
Loxodonta africana	ENSLAFG00000017749	1 retrocopy	retro_lafr_1168,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979, retro_mdom_736, retro_mdom_786, retro_mdom_979,
Mus musculus	ENSMUSG00000022674	4 retrocopies	retro_mmus_1385, retro_mmus_189, retro_mmus_2048, retro_mmus_2770,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Procavia capensis	ENSPCAG00000000293	1 retrocopy	retro_pcap_138 ,
Sus scrofa	ENSSSCG00000022190	1 retrocopy	retro_sscr_524,
Tursiops truncatus	ENSTTRG00000008325	1 retrocopy	retro_ttru_1623,