RetrogeneDB ID: retro_tsyr_404

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_11082:10293..10816(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX4
• Ensembl ID: ENSTSYG00000000602
• Aliases: None
• Description: peroxiredoxin 4 [Source:HGNC Symbol;Acc:17169]

Sequence

>retro_tsyr_404
TTCAAGGGGGTGAAGCTGTTGGACTACAAAGGGAAGCACATGGTCCTCTTTTCTACCCTCTGGACTTCACTTTTGGGTGC
CCCACGGAGATCGTCACCTTCAGTGGCCATGCTGAGGTCTTGCGCAAGCTGGGCAGCAAAGTGCTGGGAGTCTCAGTGGA
CTCTCCCAGTTCACTCACTTGGCTTGAACCCAGACCCCCCAGAAAGGAGGGAGGCTTGGGTTCCCTGAACATCCCCCACT
TGTTGATGTGACCAGAAGCTTGTCCCACGATTATGGCGTGCTGAAAAGAGATGAGGGCATTGCCTCCAGAGACCTCTCTA
TCATCGATGCCAAGGGTGTCCTTTGCCAGCTCACTGTTGATGATCTGTCCTTGGGGTGCTCCATGGATGAGGCTCTGTGG
CTTGTCCAGGCCTTCCAGTACACAGATGAGCACAGACAAGTCTGTCCCACTGGCTGGAAGCCGGACAGTGATGCGATCAA
ACCCAGCATGGATGATGGCAGGGAATACTTCTCCAAACACAAC

Alignment

ORF - retro_tsyr_404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.12 %
• Parental protein coverage: 63.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FKELKLTDYRGKYLVFF-FYPLDFTFVCPTEINAFDDRIEEFRSINTEVVACSVDSQFTHLAWI--NTPR
          FK..KL.DY.GK..V.F.FYPLDFTF.CPTEI..F....E..R.....V...SVDS....L.W.....PR
Retrocopy FKGVKLLDYKGKHMVLF<FYPLDFTFGCPTEIVTFSGHAEVLRKLGSKVLGVSVDSP-SSLTWLEPRPPR

Parental  RQGGLGPMRI-PLLSDLNHQISKDYGVYLEDSGHTLRGLFIIDDKGILRQITMNDLPVGRSVDETLRLVQ
          ..GGLG...I.P.L.D.....S.DYGV...D.G...R.L.IID.KG.L.Q.T..DL..G.S.DE.L.LVQ
Retrocopy KEGGLGSLNI<PPLVDVTRSLSHDYGVLKRDEGIASRDLSIIDAKGVLCQLTVDDLSLGCSMDEALWLVQ

Parental  AFQYTDKHGEVCPAGWKPGSETIIPDPAGKLKYFDKLN
          AFQYTD.H..VCP.GWKP.S..I.P.......YF.K.N
Retrocopy AFQYTDEHRQVCPTGWKPDSDAIKPSMDDGREYFSKHN

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_404 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006165	1 retrocopy	retro_btau_439,
Cavia porcellus	ENSCPOG00000004185	1 retrocopy	retro_cpor_353,
Equus caballus	ENSECAG00000010085	1 retrocopy	retro_ecab_576,
Homo sapiens	ENSG00000123131	1 retrocopy	retro_hsap_3165,
Gorilla gorilla	ENSGGOG00000026790	1 retrocopy	retro_ggor_1351,
Myotis lucifugus	ENSMLUG00000004904	2 retrocopies	retro_mluc_2347, retro_mluc_2619,
Macaca mulatta	ENSMMUG00000021366	1 retrocopy	retro_mmul_2001,
Tupaia belangeri	ENSTBEG00000004454	5 retrocopies	retro_tbel_2164, retro_tbel_2467, retro_tbel_2522, retro_tbel_2811, retro_tbel_2978,
Tarsius syrichta	ENSTSYG00000000602	1 retrocopy	retro_tsyr_404 ,
Tarsius syrichta	ENSTSYG00000011031	1 retrocopy	retro_tsyr_1781,
Tursiops truncatus	ENSTTRG00000012368	1 retrocopy	retro_ttru_547,