RetrogeneDB ID: retro_ogar_2368

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873615.1:4927187..4927715(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000030247
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPIH
• Ensembl ID: ENSOGAG00000014937
• Aliases: None
• Description: peptidylprolyl isomerase H (cyclophilin H) [Source:HGNC Symbol;Acc:14651]

Sequence

>retro_ogar_2368
GCGGTGGCAAATTCTAGCCCTGTCAACCCTGTACTGTTCTTTGATGTCAGCGTTGGTGGCCGGGAAGTTGGCCGCATGAA
GATCGAGCTCTTTGCAGACGTTGTGCCTAAAACAGCAGAGAACTTTAGGCAATTCTGCACTGGAGAATTCAGAAAAGATG
GGGTTCCAATAGGATACAAAGGGAGCACCTTCCACAGGGTTATAAAGGATTTCATGATTCAGGGTGGTGATTTTGTTAAT
GGAGATGGTATTGGAGTTGCCAGTATTTACCGGGGGCCATTTGCAGATGAAAAATTTAAACTTAGGCACTCTGCTCCAGG
CCTGCTTTCCATGGCAAACAATGGTCCCAGTACAAATGGCTGTCGATTCTTTATCACCTGCTCTAAGTGCGATTGGCTGG
ATGGAAAGCATGTAGTGTTTGGAAAAATCATTGATGGACTTCTAGTGATGGGAAAGATTGAGAATGTTCCCACAGGCCCC
AACAATAAGCCCAAGCTGCCTGTGGTGATCTCACAGCGTGGGGAAATG

Alignment

ORF - retro_ogar_2368 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.89 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVANSSPVNPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKD
          AVANSSPVNPV.FFDVS.GG.EVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKD
Retrocopy AVANSSPVNPVLFFDVSVGGREVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKD

Parental  FMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVF
          FMIQGGDFVNGDG.GVASIYRGPFADE.FKLRHSAPGLLSMAN.GPSTNGC.FFITCSKCDWLDGKHVVF
Retrocopy FMIQGGDFVNGDGIGVASIYRGPFADEKFKLRHSAPGLLSMANNGPSTNGCRFFITCSKCDWLDGKHVVF

Parental  GKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGEM
          GKIIDGLLVM.KIENVPTGPNNKPKLPVVISQ.GEM
Retrocopy GKIIDGLLVMGKIENVPTGPNNKPKLPVVISQRGEM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2368 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 9 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003145	5 retrocopies	retro_cjac_129, retro_cjac_1886, retro_cjac_2205, retro_cjac_3120, retro_cjac_4110,
Macropus eugenii	ENSMEUG00000001691	1 retrocopy	retro_meug_1699,
Macaca mulatta	ENSMMUG00000013129	1 retrocopy	retro_mmul_1124,
Mustela putorius furo	ENSMPUG00000013966	2 retrocopies	retro_mputfur_285, retro_mputfur_542,
Mus musculus	ENSMUSG00000060288	7 retrocopies	retro_mmus_2563, retro_mmus_2873, retro_mmus_3195, retro_mmus_3709, retro_mmus_749, retro_mmus_913, retro_mmus_977,
Otolemur garnettii	ENSOGAG00000011275	3 retrocopies	retro_ogar_1484, retro_ogar_2850, retro_ogar_939,
Otolemur garnettii	ENSOGAG00000014937	1 retrocopy	retro_ogar_2368 ,
Procavia capensis	ENSPCAG00000011139	1 retrocopy	retro_pcap_81,
Rattus norvegicus	ENSRNOG00000008489	1 retrocopy	retro_rnor_2911,