RetrogeneDB ID: retro_ogar_988

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873532.1:23363472..23364321(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM2
• Ensembl ID: ENSOGAG00000011793
• Aliases: None
• Description: tropomyosin 2 (beta) [Source:HGNC Symbol;Acc:12011]

Sequence

>retro_ogar_988
ATGGACACCATCAAGAAGAAGATACAGACGCTAAAGTTGTACAAGGAGAATGCCATCGACTGTGCTGAGCAGGCCAAGGC
AGACAAGAGGCAAGCTGAGGACCGCTGCAAGCAGCTGGAGGAGGAGCAGCAGGCCCTCCAGAAGAAGCTGGAGGGGACAG
AGGATTAGATGGAAAAGTATTCTGAATCCATGAAGGATGCCCAGGAGAAACTGGAGCAAGCTGAGAAGAGGGTGACCAAT
GCTGAAGCAGAAGTGGCCTCGAACTGTCGCATTCAGCTGGTAGAGGAGGAGCTGGATTGGGCAAAAGAGCGCTTGGCCAC
AGCCCTGCAAAAGCTGGAGGAGGCTGAGAAGTCAGCTAATGAGAGCTCGAGAGGAATGCAGGTCATTGAAAACCGGGCCA
TGAAGGATGAAGAAAAGACGGAGCTATAGGAGATGCCGCTGAAGGAGGCCAAGCACATCGCTGAGGATTCAGACTGCAAA
TACACAGAGGTGGCCAGGAAGCTGGTGATCCTGGAAGGAGAGCTGGAGCGCTCAGAAGAGAGAGCTGAGGTGGCTGAGAG
CAGAGCCAGGCAGTTGGAGGAGGAACTTTGAACCATGGACCAGGCCCTCAAGTCCCTGATGGCCTCAGAGGAGTAGTATT
CCACCAAAGAAGAGAAATATGAAGAGGAGATCAAACTGCTGGAGGAGCAGCTGAAGGAGGCTGAGACCTGAGTGGAATTT
GCTGAAAGGTCTGTGGCAAAGCTGGAGAAAACCACTGATGACCTAGAAGAGATCTTGGCCAGTGCCAAGGAGGAGAAGGT
GGAGATTCACCAGACCCTGGACCAGATCCTGCTGGAACTCAACAGCCTG

Alignment

ORF - retro_ogar_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDAIKKKMQMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEKYSESVKDAQEK
          MD.IKKK.Q.LKL.KENAID.AEQA.ADK.QAEDRCKQLEEEQQ.LQKKL.GTED..EKYSES.KDAQEK
Retrocopy MDTIKKKIQTLKLYKENAIDCAEQAKADKRQAEDRCKQLEEEQQALQKKLEGTED*MEKYSESMKDAQEK

Parental  LEQAEKKATDAEAEVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIENRAMKDEEK
          LEQAEK..T.AEAEVAS.N.RIQLVEEELD.A.ERLATALQKLEEAEK.A.ES.RGM.VIENRAMKDEEK
Retrocopy LEQAEKRVTNAEAEVAS-NCRIQLVEEELDWAKERLATALQKLEEAEKSANESSRGMQVIENRAMKDEEK

Parental  MELQEMQLKEAKHIAEDSDRKYEEVARKLVILEGELERSEERAEVAESRARQLEEELRTMDQALKSLMAS
          .EL.EM.LKEAKHIAEDSD.KY.EVARKLVILEGELERSEERAEVAESRARQLEEEL.TMDQALKSLMAS
Retrocopy TEL*EMPLKEAKHIAEDSDCKYTEVARKLVILEGELERSEERAEVAESRARQLEEEL*TMDQALKSLMAS

Parental  EEEYSTKEDKYEEEIKLLEEKLKEAETRAEFAERSVAKLEKTIDDLEETLASAKEENVEIHQTLDQTLLE
          EE.YSTKE.KYEEEIKLLEE.LKEAET..EFAERSVAKLEKT.DDLEE.LASAKEE.VEIHQTLDQ.LLE
Retrocopy EE*YSTKEEKYEEEIKLLEEQLKEAET*VEFAERSVAKLEKTTDDLEEILASAKEEKVEIHQTLDQILLE

Parental  LNNL
          LN.L
Retrocopy LNSL

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_988 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009627	2 retrocopies	retro_cjac_1839, retro_cjac_1894,
Otolemur garnettii	ENSOGAG00000011793	1 retrocopy	retro_ogar_988 ,
Otolemur garnettii	ENSOGAG00000025133	1 retrocopy	retro_ogar_62,
Rattus norvegicus	ENSRNOG00000016731	1 retrocopy	retro_rnor_1520,