RetrogeneDB ID: retro_tbel_1243

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_423:182984..183250(+)
• Located in intron of: ENSTBEG00000003638

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOC1
• Ensembl ID: ENSTBEG00000007093
• Aliases: None
• Description: apolipoprotein C-I [Source:HGNC Symbol;Acc:607]

Sequence

>retro_tbel_1243
ATGAGGCTCCTCCTGTGGCTCCCAGTCCTGCCGGTGGTTCTGTAAGTGTTTTTGGAAGGCCCACATCCAGCCCAGGCAGT
CCCAGACACATCCAGCAACTCGGAGGGCCTCCTGGATAAGCTGAAGCAGTTTGGAAACGCCCTGGAGGACAAGACCATTA
AAAAGCTACTGAATGTATCGAGCAGAGTGACCTTCCTGCCAAGACCCAGAACTGGTTTTCAGAGACATTTGGCAAAGTGA
GAGATGAACTCAAAGCTACGTTCTCC

Alignment

ORF - retro_tbel_1243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLLLSLPVLLVALSVVLEGPAPAQAAPDFSSTLEGLPDKLKEFGNTLEDKA-KK-AIERIKQSDLPAKT
          MRLLL.LPVL.V.L.V.LEGP.PAQA.PD.SS..EGL.DKLK.FGN.LEDK..KK.A.E.I.QSDLPAKT
Retrocopy MRLLLWLPVLPVVL*VFLEGPHPAQAVPDTSSNSEGLLDKLKQFGNALEDKTIKK<ATECIEQSDLPAKT

Parental  RNWFTETFGKVRDTFKATFS
          .NWF.ETFGKVRD..KATFS
Retrocopy QNWFSETFGKVRDELKATFS

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_1243 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1243 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012737	1 retrocopy	retro_amel_582,
Canis familiaris	ENSCAFG00000004615	1 retrocopy	retro_cfam_530,
Otolemur garnettii	ENSOGAG00000028159	1 retrocopy	retro_ogar_2801,
Rattus norvegicus	ENSRNOG00000018426	1 retrocopy	retro_rnor_204,
Tupaia belangeri	ENSTBEG00000007093	2 retrocopies	retro_tbel_1243 , retro_tbel_2226,