RetrogeneDB ID: retro_tbel_3415

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_139666:61945..62373(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TACO1
• Ensembl ID: ENSTBEG00000017006
• Aliases: None
• Description: translational activator of mitochondrially encoded cytochrome c oxidase I [Source:HGNC Symbol;Acc:24316]

Sequence

>retro_tbel_3415
CTGAACATCCGCCTGGCAGTTAAAGAGGGAGCCGTCAACCCCGAGCTCAGAGACAACCTGACCAGCATTTTGAGAGGTGT
GTCACAACAAGCCCGTCCCCAAGTCAACAATTGAGGCAGCGCTGAAAATGGAGAAATCTAAGGACACTTACTTGCTGAGT
GAGGGTAGAGCTGTGGTGGCTCTTCTCTGCATTTTTAGGCATTATCGAGCTGTGACTCCCAGTGCCTGTGGGACGTTAGA
CATATCCTGAACTAGAACAGGAGGGATGATGGCTAAATGGAGTTAGTCACTCAGGGTTGGTTGTAGTTGGAGTAGGGGAT
AGGGAGAAGAAAACTGTGAACCTAGAGCATGCCCTGGAGCCGGCATTCAAAGCCAGGAGCTCTCAGGATGTCAAGGAAAC
CAAGGTGGAGGAAGAAAAGTACCATTTT

Alignment

ORF - retro_tbel_3415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 63.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LNIRLAVKEGGPNPELNSNLASIL-EVCRSKHMPKSTIEAALKVEKSKGTYLLYEGRGP-GGSSLLIEAL
          LNIRLAVKEG..NPEL..NL.SIL.EVC..K..PKSTIEAALK.EKSK.TYLL.EGR...GGSSL...AL
Retrocopy LNIRLAVKEGAVNPELRDNLTSIL>EVCHNKPVPKSTIEAALKMEKSKDTYLLSEGRAV<GGSSLHF*AL

Parental  SNSGPKCLSDIRHILN-KNGGMMAE-GARHSFDKKGVVVVGVEDREKKTVNLERALELAFEA-GAEDVKE
          S.....CL.D.RHILN...GGMMA..G..HS....G.VVVGV.DREKKTVNLE.ALE.AF.A....DVKE
Retrocopy SSCDSQCLWDVRHILN>RTGGMMAK>GVSHS----GLVVVGVGDREKKTVNLEHALEPAFKARSSQDVKE

Parental  TEDEEEKNIF
          T..EEEK..F
Retrocopy TKVEEEKYHF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3415 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3415 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 ,