RetrogeneDB ID: retro_tsyr_852

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_21812:2619..3074(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTPA
• Ensembl ID: ENSTSYG00000003052
• Aliases: None
• Description: tocopherol (alpha) transfer protein [Source:HGNC Symbol;Acc:12404]

Sequence

>retro_tsyr_852
TTACTAAAAAATTATTATAAGTGGAGAGCAGAATGTCCAGAAATAAGTGCAGATCTGCACCCTAGAAGTATTCTTGGCCT
TCTGAAGGCTGGCTACCATGGAATCCTAAGATCTAGGGATCCCACTGGCAGCAAAGTTCTTATTTACAGACTCACACACT
GGGACCCAAAAGTTTTTAGAGCTTATGATGTATTTCATGTAAGTCTAATCACATCCAAGCTTATTGTACGGGAGGTAGAA
ACTCAACGGAATGAAATCAAGGCTACCTTTATCTGGAAGGCTGGCAGTTTTCTCATGCTTTTCAAATTACCCCATATGTA
GCTAAGAAGATTGCTGCTGTACTTACAGATTCCTTTCCATTGAAAGTTTGTGGCATCCATTTGATAAATGAACAAGTAAT
TTTCCATGCTGTCTTTTCCATGATTAAACCATTCCTGACTGAAAAAATTAAGGAA

Alignment

ORF - retro_tsyr_852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.5 %
• Parental protein coverage: 72.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLKNYYKWRAECPEISADLHPRSILGLLKAGYHGVLRSRDPTGSKVLIYRIAHWDPKVFTAYDVFRVSLI
          LLKNYYKWRAECPEISADLHPRSILGLLKAGYHG.LRSRDPTGSKVLIYR..HWDPKVF.AYDVF.VSLI
Retrocopy LLKNYYKWRAECPEISADLHPRSILGLLKAGYHGILRSRDPTGSKVLIYRLTHWDPKVFRAYDVFHVSLI

Parental  TSELIVREVETQRNGIKAIF-DLEGWQFSHAFQITPSVAKKIAAVLTDSFPLKVRGIHLINEPVIFHAVF
          TS.LIVREVETQRN.IKA.F..LEGWQFSHAFQITP.VAKKIAAVLTDSFPLKV.GIHLINE.VIFHAVF
Retrocopy TSKLIVREVETQRNEIKATF<YLEGWQFSHAFQITPYVAKKIAAVLTDSFPLKVCGIHLINEQVIFHAVF

Parental  SMIKPFLTEKIKE
          SMIKPFLTEKIKE
Retrocopy SMIKPFLTEKIKE

Legend:

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

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_852 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000000305	1 retrocopy	retro_mmur_1594,
Tarsius syrichta	ENSTSYG00000003052	1 retrocopy	retro_tsyr_852 ,