RetrogeneDB ID: retro_tsyr_1061

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_29374:22886..23510(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPX6
• Ensembl ID: ENSTSYG00000000641
• Aliases: None
• Description: glutathione peroxidase 6 (olfactory) [Source:HGNC Symbol;Acc:4558]

Sequence

>retro_tsyr_1061
CTGCTCTCCCTGCTCCTGGTCGGTTTCGCACCGCCCAGTCACAGGCAGGGGAAGTCCAAGATGGACTGTCACAGCGGCGT
GAGGGGCACCATCTGCGAGTACGGAGCACTCACCTTTGATGGGGAGGAGTATATCCCCTTCGAGCAGTACGCAGGCAAAT
ACGTCCTCTTTGTCAATGTGGCCAGCTACTGAGGCCTGATGGGCCAGTACGTGGAACTGAATGCACTACAGGAGGAGCTG
GCCCCGTTGGGTCTGGTCACTCTGGGCTTCCCCTGCAACCAATTCGGAAAACAAGAACCAGGAGAGAACTCTGAAATCCT
TCCCAGTCTCAAGTATGTCCGCCCCAGCGGGCACTACGTTCCCAATTTCCAGCCTTTGGAGAAAGGAGATGTGAACCGAG
AGAAAGAGTAGAAGTTCTGCACCTTCCTGAAGAACCCCTGTCTTCCCACCTCGGAGTTCCTGGGCTCCCCTGACTGCCTC
TTCTGGGAACCCGTGAAGGCCCACGACATCTGCTGGAATTTTGAGAAGTTGCTGGTGGGCCCAGATGGTAAACTCGTTAT
GCGCTGGTACCACCCGACCACGGTCAGCAACGTCAAGATGGGCATTCCTTCTTACATGCGGCGG

Alignment

ORF - retro_tsyr_1061 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.46 %
• Parental protein coverage: 94.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFPLFLVGFAQQTLKPQNMKVDCNKEVTGTIYEYGALTLNGEEYIQFKQYAGKHVLFVNVATYUGLAAQY
          L..L.LVGFA.........K.DC...V.GTI.EYGALT..GEEYI.F.QYAGK.VLFVNVA.Y.GL..QY
Retrocopy LLSLLLVGFAPPSHRQGKSKMDCHSGVRGTICEYGALTFDGEEYIPFEQYAGKYVLFVNVASY*GLMGQY

Parental  PELNALQKELKNFDVIVLGFPCNQFGKQEPGTNSEILPGLKYVRPGGGFVPNFQLFEKGDVNGEKT-KVF
          .ELNALQ.EL.......LGFPCNQFGKQEPG.NSEILP.LKYVRP.G..VPNFQ..EKGDVN.EK..K..
Retrocopy VELNALQEELAPLGLVTLGFPCNQFGKQEPGENSEILPSLKYVRPSGHYVPNFQPLEKGDVNREKE*KFC

Parental  TFLNNSCPPTSDLLGSSSQLFWEPMKVHDIRWNFEKFLVGPNGVPVKRWFHRAPVSTVKSDILDYLKQ
          TFL.N.C.PTS..LGS...LFWEP.K.HDI.WNFEK.LVGP.G..V.RW.H...VS.VK..I..Y...
Retrocopy TFLKNPCLPTSEFLGSPDCLFWEPVKAHDICWNFEKLLVGPDGKLVMRWYHPTTVSNVKMGIPSYMRR

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_1061 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007526	1 retrocopy	retro_chof_347,
Tarsius syrichta	ENSTSYG00000000641	1 retrocopy	retro_tsyr_1061 ,
Tarsius syrichta	ENSTSYG00000012413	2 retrocopies	retro_tsyr_1170, retro_tsyr_2159,