RetrogeneDB ID: retro_tbel_2016

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_670:94354..94674(+)
• Located in intron of: ENSTBEG00000015843

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM243
• Ensembl ID: ENSTBEG00000007846
• Aliases: None
• Description: transmembrane protein 243, mitochondrial [Source:HGNC Symbol;Acc:21707]

Sequence

>retro_tbel_2016
AGTGGCCTGGACAACAGACCCCTGTTCAGGGAGACATTGGCGAAGGATCAAATCATCAATCGAGTAGTTTGCAGCCTGAC
ATCCTTACGATTCTAGTAATGCTGATTAGTGATTTTGTTTTCCCTCAACTACCTCCAAAGCCATTGAATGCATTTTTTGC
TGTCTGCATCCCTTTAAGTAGTAGTACTGCCTGCACACTTATTTACTGGTATCGACAAGGAGACTTAGAGCTGAAATTTA
GAAAGCTAATTTACTGTATCTTATTTTGTATCATCATGTTATGTGTATGTGCAAATCTGTATGTTCATGATGTGGGAAGG

Alignment

ORF - retro_tbel_2016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGLDNRPLFGETSAKDRIINLVVGILTSL-LILVTLISAFVFPQLPPKPLNIFFAVCISLSSITACILIY
          SGLDNRPLF.ET.AKD.IIN.VV..LTSL..ILV.LIS.FVFPQLPPKPLN.FFAVCI.LSS.TAC.LIY
Retrocopy SGLDNRPLFRETLAKDQIINRVVCSLTSL<TILVMLISDFVFPQLPPKPLNAFFAVCIPLSSSTACTLIY

Parental  WYRQGDLEPKFRKLIYYILFCIIMLCICANLYFHDVGR
          WYRQGDLE.KFRKLIY.ILFCIIMLC.CANLY.HDVGR
Retrocopy WYRQGDLELKFRKLIYCILFCIIMLCVCANLYVHDVGR

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_2016 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2016 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004888	4 retrocopies	retro_chof_1660, retro_chof_175, retro_chof_1906, retro_chof_821,
Microcebus murinus	ENSMICG00000014707	1 retrocopy	retro_mmur_808,
Otolemur garnettii	ENSOGAG00000000023	2 retrocopies	retro_ogar_1800, retro_ogar_383,
Rattus norvegicus	ENSRNOG00000042758	1 retrocopy	retro_rnor_2506,
Sorex araneus	ENSSARG00000002439	1 retrocopy	retro_sara_32,
Tupaia belangeri	ENSTBEG00000007846	3 retrocopies	retro_tbel_2016 , retro_tbel_2828, retro_tbel_4176,