RetrogeneDB ID: retro_tbel_4734

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_99639:16878..17342(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRUB2
• Ensembl ID: ENSTBEG00000000586
• Aliases: None
• Description: TruB pseudouridine (psi) synthase homolog 2 (E. coli) [Source:HGNC Symbol;Acc:17170]

Sequence

>retro_tbel_4734
CTCGGCGTGGGGCGGGGATGCAGGCTCCCCACTGACATGTCCGATGCTCATCTCACTAAGGATTACACGGTGCATGGCGT
CCTAGGCAAGGCCACATACGACCTCCATGATGCTGGGCGGCTAGTGGAGAAGACAGCATATGGCCATGTGACCGGAGGGG
AGCTAGACCAGGTCCTGGCTATGATCCAAGGCTCCCACCAGACGGCCCTGCTGATGTAGTCCAACTTCCACCTGAAGACT
CGGGGGGCCTACGAGATGGCCGTGAGGGGCTTGATCCGACCCAGGAACCAGTCCCTGATGCTGGTAACCGGCATCGATGC
TGCCACTTCTCACCTCCAGAGCTCGTCTTAGAGGTGCAGTGCCTGCATGAAACACCACAGCAGCTGCGCGGACTGGGGCA
CGAGGTCGGCCTGGAGCTGAAGACCAGCGCTGTCAGCTCCCAGGTGCGGCACACATGCGACGGT

Alignment

ORF - retro_tbel_4734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 68.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGVGRGCRLLTDMYDAHLTKDYTVHGILGKATDDFREDGRLVEKTTYDHVTRGKLDRVLAVIQGSHPEAL
          LGVGRGCRL.TDM.DAHLTKDYTVHG.LGKAT.D....GRLVEKT.Y.HVT.G.LD.VLA.IQGSH..AL
Retrocopy LGVGRGCRLPTDMSDAHLTKDYTVHGVLGKATYDLHDAGRLVEKTAYGHVTGGELDQVLAMIQGSHQTAL

Parental  VMYSNLDLKTQEAYEMAVRGLIRPRNKSPMLVTGI-QCCHFAPPEFVLEVQCLHETPQQLRKLVHEVGLE
          .M.SN..LKT..AYEMAVRGLIRPRN.S.MLVTGI..CCHF.PPE.VLEVQCLHETPQQLR.L.HEVGLE
Retrocopy LM*SNFHLKTRGAYEMAVRGLIRPRNQSLMLVTGI<RCCHFSPPELVLEVQCLHETPQQLRGLGHEVGLE

Parental  LKTSAVCSQVRRTRDG
          LKTSAV.SQVR.T.DG
Retrocopy LKTSAVSSQVRHTCDG

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_4734 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4734 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000009114	1 retrocopy	retro_etel_1975,
Otolemur garnettii	ENSOGAG00000003511	2 retrocopies	retro_ogar_440, retro_ogar_441,
Tupaia belangeri	ENSTBEG00000000586	1 retrocopy	retro_tbel_4734 ,