RetrogeneDB ID: retro_ogar_2288

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873609.1:3667075..3667652(-)
• Located in intron of: ENSOGAG00000013536

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSOGAG00000014002
• Aliases: None
• Description: programmed cell death 2 [Source:HGNC Symbol;Acc:8762]

Sequence

>retro_ogar_2288
TGCCCCAGGGCTCATTACTGCGGTTAGGCGCATCAGACTCTCCATTGGAGATAGGACATAAGCAGGCCTGTTCACAGCCC
ATCACTTGGACCATGCAAGTCCAGACCACAACTTCCTTTTCCACAATTTGAAATTGTGTTAGGTAGAAGATGAGATTATG
CCTGAAGTTGTAGAAAAGGAAGATGCTGGGGGATTGTGGGGACTGTGGGTGAAGCACTTGAGGAAGAACTAGATTCCATG
GCACAACTTGAATACATGGAAGATATAATTTTCCAGAAGTTTAAAACTCAAATAGCTCTTGAACCAGTTGAGATTCTCAG
ATCTAGCAGAGGTCTTACCCCTATCTGGATTTCTGGTGAAAATATCTCTCAAGAAAAGGATATTCTAGACTGCCCCTATG
GTACCAAGAGAATATTTGAATTCCAGGTTGTGCTCAGCTGATGAACCACTTGCAGGATGACAGACTGGGTGCCCGTGTGG
GCTGGGGGTCCTGGCTGCCTTCGCCTGTGCTGAGACCTGTGGCTTGGTTACTGGCGATGCAGAGGAATTTGTGTGAAAGT
CAGATATAATAGATACA

Alignment

ORF - retro_ogar_2288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.5 %
• Parental protein coverage: 56.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  CHKVHYCGKVHQALDWR-LGHKQACSQP-DHLDHGIPDHNFLFPEFEIIIETEDDIMPEVMGEEDATE-I
          C...HYCG..HQ.L.WR..GHKQACSQP..HLDH..PDHNFLF.........ED.IMPEV...EDA...I
Retrocopy CPRAHYCG*AHQTLHWR<IGHKQACSQP<HHLDHASPDHNFLFHNLKLC*-VEDEIMPEVVEKEDAGG<I

Parental  VGSMGETLEEELDSMAKHESREDKIFQKFKTHIALDPEQILRYGRGLAPIWISGENIPEEKDIPDCPCGA
          VG..GE.LEEELDSMA..E..ED.IFQKFKT.IAL.P..ILR..RGL.PIWISGENI..EKDI.DCP.G.
Retrocopy VGTVGEALEEELDSMAQLEYMEDIIFQKFKTQIALEPVEILRSSRGLTPIWISGENISQEKDILDCPYGT

Parental  KRIFEFQVM-PQLLNYLKADRLGTSVDW-GVLAVFTCAESCSLGTGYTEEFVWKQDVTDT
          KRIFEFQV...QL.N.L..DRLG..V.W.GVLA.F.CAE.C.L.TG..EEFV.K.D..DT
Retrocopy KRIFEFQVV<AQLMNHLQDDRLGARVGW<GVLAAFACAETCGLVTGDAEEFV*KSDIIDT

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_2288 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017075	2 retrocopies	retro_amel_1329, retro_amel_1404,
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Equus caballus	ENSECAG00000016819	1 retrocopy	retro_ecab_533,
Felis catus	ENSFCAG00000007037	2 retrocopies	retro_fcat_305, retro_fcat_749,
Homo sapiens	ENSG00000071994	1 retrocopy	retro_hsap_4305,
Gorilla gorilla	ENSGGOG00000028229	2 retrocopies	retro_ggor_2876, retro_ggor_899,
Microcebus murinus	ENSMICG00000007474	1 retrocopy	retro_mmur_108,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Mustela putorius furo	ENSMPUG00000007227	2 retrocopies	retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys	ENSNLEG00000000295	2 retrocopies	retro_nleu_1458, retro_nleu_2633,
Otolemur garnettii	ENSOGAG00000014002	2 retrocopies	retro_ogar_2090, retro_ogar_2288 ,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Pan troglodytes	ENSPTRG00000018828	2 retrocopies	retro_ptro_2915, retro_ptro_788,
Pteropus vampyrus	ENSPVAG00000010822	1 retrocopy	retro_pvam_1150,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,