RetrogeneDB ID: retro_tbel_2811

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_119693:172478..172949(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX4
• Ensembl ID: ENSTBEG00000004454
• Aliases: None
• Description: peroxiredoxin 4 [Source:HGNC Symbol;Acc:17169]

Sequence

>retro_tbel_2811
GCACCCTACTTTAAGGGTATAGCTGTTGTCAAAGGAGAGTTCAAAGACCTAAGTCTTGATGACTTTAAGGGGAAATATTT
GGTGCTTTTCTTCTATCCTTTGGATTTCACCTTCGTGTGTCCTACAGAAATTACTGTTTTTAGTGACAAAGTAAATGAAT
TTCATGACGTGAATTATGAAGTCATTGCAGTTTCAGTGAACTCCCAATTTAGCCATCTTGCCTGGATAAATACATCAAGG
AAGAATGGTGGTTTGGGCCACATGAGGCATCGCACTCTTGTCCGATTCAACTAAACAAATTTCTCTAGACTACAATGTGC
TGTTAGAAGGTCCAGTTCTTGTACTACGAGGTCCTTCATAATTGACTCCAATGGAATCATCAAGCACCTGAGTGTCAATG
ATCTTCCAGTGGGCCCAAGCGTGTTAGAGACCCTTCACTTGATGAAGGCATCCCAGTTTGTGGAAAGCCAT

Alignment

ORF - retro_tbel_2811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.38 %
• Parental protein coverage: 96.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  APYWEGTAVINGEFKELKLTDYRGKYLVFFFYPLDFTFVCPTEIIAFGDRIEEFRSINTEVVACSVDSQF
          APY..G.AV..GEFK.L.L.D..GKYLV.FFYPLDFTFVCPTEI..F.D...EF...N.EV.A.SV.SQF
Retrocopy APYFKGIAVVKGEFKDLSLDDFKGKYLVLFFYPLDFTFVCPTEITVFSDKVNEFHDVNYEVIAVSVNSQF

Parental  THLAWINTPRRQGGLGPIK-IPLLSDLTHQISKDYGVYLEDSGHTLRG-LFIIDDKGILRQITLNDLPVG
          .HLAWINT.R..GGLG....I.LLSD.T.QIS.DY.V.LE.....LRG..FIID..GI......NDLPVG
Retrocopy SHLAWINTSRKNGGLGHMR>IALLSDSTKQISLDYNVLLEGPVLVLRG<SFIIDSNGIIKHLSVNDLPVG

Parental  RSVDETLRLVQAFQYTDKH
          .SV.ETL.L..A.Q....H
Retrocopy PSVLETLHLMKASQFVESH

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_2811 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2811 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 12 parental genes, and 24 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,
Tupaia belangeri	ENSTBEG00000011064	5 retrocopies	retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tupaia belangeri	ENSTBEG00000015997	4 retrocopies	retro_tbel_3922, retro_tbel_4017, retro_tbel_4024, retro_tbel_4669,
Tarsius syrichta	ENSTSYG00000000602	1 retrocopy	retro_tsyr_404,
Tursiops truncatus	ENSTTRG00000012368	1 retrocopy	retro_ttru_547,