RetrogeneDB ID: retro_ogar_687

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873525.1:29976075..29976502(-)
• Located in intron of: ENSOGAG00000011302

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM56
• Ensembl ID: ENSOGAG00000002403
• Aliases: None
• Description: transmembrane protein 56 [Source:HGNC Symbol;Acc:26477]

Sequence

>retro_ogar_687
ATTGGTGACAAATTGTTTATAATTCCCCATCGGGCAGTGCTGTATGTGTACTTCTTTGTATTCAAAATATGGAGTGCTGG
CCTACTCTGGGAATTTCTGCCCGCTTGCAGAACTTTCCAGCACTTCTGCAAATCAGTAGTGGTTCTCTGAAGCCCTGAAA
TACCCTAAGTTTTCCAAAGCTCATGTCATCAATGGAACACTTGTGACAGTGGTGTTCTTCATCATGTGGATTGCCTCAAT
GCCTCCTTTGTACAGCTTCATGTATTCTGTGTAAGGAAGAGAACCCTACAGAAGGCTTGGATTATTAATCTAATTTTCCT
GGATTGCTTCCTGTATTGTTTTAGATATGATGAATGTCATGCGAATGATCAAAATTTCAAAAGGGTGCATCAGTTGTCTT
TTCCTTCAGACAAGAGAAAGCCCCAAA

Alignment

ORF - retro_ogar_687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.34 %
• Parental protein coverage: 53.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IGDKFFIVHHCAALYAYFFLLK-EGVLAYIGNFRLLAELSSPFVNQRWFFEALKYPKFCTANVVNGILMM
          IGDK.FI..H.A.LY.YFF..K..GVLAY.GNF..LAELSS...NQ.WF.EALKYPKF..A.V.NG.L..
Retrocopy IGDKLFIIPHRAVLYVYFFVFK>YGVLAYSGNFCPLAELSSTSANQ*WFSEALKYPKFSKAHVINGTLVT

Parental  VVFFLVRVASMPPLYGFMYSVYGTEPYERLGLVIQCSWIASCVILDVMNIMWMIKISKGCIKVVSLFRKE
          VVFF....ASMPPLY.FMYSV.G.EPY.RLGL.I..SWIASC..LD.MN.M.MIKISKGCI....L...E
Retrocopy VVFFIMWIASMPPLYSFMYSV*GREPYRRLGLLI*FSWIASCIVLDMMNVMRMIKISKGCISCLFLQTRE

Parental  KAR
          ...
Retrocopy SPK

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_687 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018153	1 retrocopy	retro_cjac_1354,
Otolemur garnettii	ENSOGAG00000002403	1 retrocopy	retro_ogar_687 ,