RetrogeneDB ID: retro_ogar_1737

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873563.1:667774..668190(-)
• Located in intron of: ENSOGAG00000027104

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP3S2
• Ensembl ID: ENSOGAG00000030982
• Aliases: None
• Description: adaptor-related protein complex 3, sigma 2 subunit [Source:HGNC Symbol;Acc:571]

Sequence

>retro_ogar_1737
CTTATGGTTTTCAGTAACTGTGGGAAGCTGAGGCTAGTCCATTTCTACCAGAAGTTACCAGAAGAAATTCAACAGCAGAT
GGGTGGTTCGGGAGACTTTCCATTTAGTCCTAAAGCAGGATGACAACATCTGTAACTTCTTCAAGAGTAAAAGATTGATT
AGTGGTTCTGACTACAAACTAATTTACTGACACTATACTACCCTCTCCTGTGTATTTTGTGTTGATTTGTCAGAGAATAA
ACTTGGGACCTTGGACCTCATCCAGGTTTTTTGTAGAGATTCTGGATAAGTGTTTCGAAAATATGTGTGAATTGGGTTTT
GTTGTCCACATGGATGACACTATGTCCTCTAGGAGGTGGTGATTTGTGGGATGGTGTTGGAAACAAACATGAATGGAAAT
CATAGCTGAGATTGAA

Alignment

ORF - retro_ogar_1737 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.73 %
• Parental protein coverage: 71.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ILVFNNHGKPRLVRFYQRFPEEI-QQQ-IVRETFHLVLKRDDNICNFLEGGSLIGGSDYKLIYRHYATLY
          ..VF.N.GK.RLV.FYQ..PEEI.QQ...VRETFHLVLK.DDNICNF.....LI.GSDYKLIY.HY.TL.
Retrocopy LMVFSNCGKLRLVHFYQKLPEEIQQQM>VVRETFHLVLKQDDNICNFFKSKRLISGSDYKLIY*HYTTLS

Parental  FVFCVDSSESELGILDLIQV-FVETLDKCFENVCELDLIFHMDKV-HYILQEVVMGGMVLETNMN-EIVA
          .VFCVD.SE..LG.LDLIQV.FVE.LDKCFEN.CEL....HMD.........V..G.MVLETNMN.EI.A
Retrocopy CVFCVDLSENKLGTLDLIQV>FVEILDKCFENMCELGFVVHMDDT<YVL*EVVICG-MVLETNMN>EIIA

Parental  QIE
          .IE
Retrocopy EIE

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_1737 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 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001407	1 retrocopy	retro_btau_436,
Choloepus hoffmanni	ENSCHOG00000003359	4 retrocopies	retro_chof_1775, retro_chof_194, retro_chof_434, retro_chof_88,
Dipodomys ordii	ENSDORG00000004247	1 retrocopy	retro_dord_115,
Equus caballus	ENSECAG00000024044	1 retrocopy	retro_ecab_549,
Felis catus	ENSFCAG00000028122	1 retrocopy	retro_fcat_311,
Macropus eugenii	ENSMEUG00000003421	1 retrocopy	retro_meug_2032,
Monodelphis domestica	ENSMODG00000019522	1 retrocopy	retro_mdom_316,
Nomascus leucogenys	ENSNLEG00000011780	2 retrocopies	retro_nleu_1380, retro_nleu_1555,
Otolemur garnettii	ENSOGAG00000030982	1 retrocopy	retro_ogar_1737 ,
Otolemur garnettii	ENSOGAG00000032376	1 retrocopy	retro_ogar_1005,
Rattus norvegicus	ENSRNOG00000043141	1 retrocopy	retro_rnor_931,
Sus scrofa	ENSSSCG00000030174	7 retrocopies	retro_sscr_1109, retro_sscr_199, retro_sscr_268, retro_sscr_339, retro_sscr_620, retro_sscr_721, retro_sscr_753,
Tursiops truncatus	ENSTTRG00000015554	2 retrocopies	retro_ttru_1233, retro_ttru_1361,
Vicugna pacos	ENSVPAG00000008668	1 retrocopy	retro_vpac_54,