RetrogeneDB ID: retro_ogar_1004

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873533.1:26860702..26861240(+)
• Located in intron of: ENSOGAG00000013851

Retrocopy information

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

Parental gene information

• Parental gene symbol: TACO1
• Ensembl ID: ENSOGAG00000006859
• Aliases: None
• Description: translational activator of mitochondrially encoded cytochrome c oxidase I [Source:HGNC Symbol;Acc:24316]

Sequence

>retro_ogar_1004
GTGTGTCGCAGCAAGCACATGCCCTAGTCAGCAATTGAAGCAGCAATGAAAATGGAGAAAACTAAAGACATACACATTTG
CTGTAAGGGTCGAGGCCCTGGTGGCTCTCCTCTGCTCATTGAGAGGCATTGTCTAACAGGAGCTCCAAGGGACAGTCAGA
CATTAGACATATCCTAAAACAAAATGGGGGCGTGATGACTGAAAGAACTCGTCACTCCTTTGAGAAAAACGGGGTGATCA
TGGTTGGAGTGGAGGACAAAGAGAAGAAAACTGTGAACCTAGAGCTGGCAATTGAAGCAGGAGCTGAGGATGTCAAGGAA
ACTGAAGATGAAGAACATTTTCAAATTTGTAATGTTTCTTCACTGCATCAGTGAGGAAGAAGTTGGACTCCCTGGGCCTG
TGTTCTATATCCTGTACTCTGGAATTCATTCCCAACTCAAAGGTGTAGCTGGCTTACCCTGACCTGGAACAGGCTGCTCA
TCTCATCCAGTTTCTCAGCAACCATGAGGACATGATCCACATCTATGACAACACTGAG

Alignment

ORF - retro_ogar_1004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.47 %
• Parental protein coverage: 62.96 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VCRSKHM-PKSTIEAALKMEKTKDM-YLLYEGRGPGGSSLLIEALSNSSSKCQSDLRHILNKNGGVMTEG
          VCRSKHM.P........K..K.K....LL...R....SS...EALSN.SSK.QSD.RHIL..NGGVMTE.
Retrocopy VCRSKHM>PSQQLKQQ*KWRKLKTY>HLL*GSRPWWLSSAH*EALSNRSSKGQSDIRHILKQNGGVMTER

Parental  ARHSFDKKGVIVVGVEDKEKKTVNLERALELAIEAGAEDVKETEDEEEKNIFKFICDVSSLHQ-VRKKLD
          .RHSF.K.GVI.VGVEDKEKKTVN....LELAIEAGAEDVKET...E....F..IC.VSSLHQ.VRKKLD
Retrocopy TRHSFEKNGVIMVGVEDKEKKTVN----LELAIEAGAEDVKET---EDEEHFQ-ICNVSSLHQ<VRKKLD

Parental  SLGLCSVSCTLEFIPNSKVQLADPDLEQAAHLIQLLSNHEDVIHVYDNIE
          SLGLCS.SCTLEFIPNSKV.LA.PDLEQAAHLIQ.LSNHED.IH.YDN.E
Retrocopy SLGLCSISCTLEFIPNSKV*LAYPDLEQAAHLIQFLSNHEDMIHIYDNTE

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_1004 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012635	1 retrocopy	retro_mluc_2236,
Otolemur garnettii	ENSOGAG00000006859	1 retrocopy	retro_ogar_1004 ,
Tupaia belangeri	ENSTBEG00000017006	1 retrocopy	retro_tbel_3415,