RetrogeneDB ID: retro_tbel_2344

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109250:103434..104021(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000000172
• Aliases: None
• Description: None

Sequence

>retro_tbel_2344
TACTTAAGGGAGATTCAGGATTCCCCCCCAGCTTGTCCCAACGACATGAACTTACTGGAAATGGACAACCTGAAAGATGA
GATGGGCAAATTCAAGAAGATGCCAGACGCTATCCCATCACTAGTGGTCTGCTACAGTGACATCAAGGAAAGCAACATCT
TGCTGCTCTCAGATCCAGAAAGTGCAGACAGCCTCATGCTGGTGGACTTTGTGTATAGCAGTTATAACTACAGGGGCTAT
GACATTGAGAACCATTTCTGTGACTGGGTTTATGATTATACTTATGAGGAATAGTCCTTCCACAAAACACAGCCCACAGA
TTACCCCACTCAGAGACAGCAGCTCCATTTTCTTTGCCATAACCTGGCATATGTAAAAAAAAAGTGAGACTCGCTCTCAA
GAGGAGCAGAAACAGCTGGAAGAAGGTTTGCTGGTGGAGATCAATTGGTATGCTCTGGTATTGCATTTCTACTGGGGCCT
GTGATCCATCCTCCAGGCATTCATGTTGACCATAGTATTTGGCTACTTTGAGTTGCCCAGTCTTGTTGCAGTTCTACTTC
TAGCAGAAAGGGCATCTGATCAGCTTC

Alignment

ORF - retro_tbel_2344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.0 %
• Parental protein coverage: 98.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YLKQIQDLSPTGPPDTNLLEMYNLKDEMGNLRKLLDSTPSPVVFCHNDIQEGNILLLSDPGSADNLMLVD
          YL..IQD..P..P.D.NLLEM.NLKDEMG...K..D..PS.VV.C..DI.E.NILLLSDP.SAD.LMLVD
Retrocopy YLREIQDSPPACPNDMNLLEMDNLKDEMGKFKKMPDAIPSLVV-CYSDIKESNILLLSDPESADSLMLVD

Parental  FEYSSYNYRGFDIGNHFCEWVYDYTHEEWPFYKAQ-PTDYPTQEQQLHFIRHYLAEVKKGEILSQEEQKK
          F.YSSYNYRG.DI.NHFC.WVYDYT.EE..F.K.Q.P...P.......F...........E..SQEEQK.
Retrocopy FVYSSYNYRGYDIENHFCDWVYDYTYEE*SFHKTQ>PQITPLRDSSSIFFAITWHMXXXXETRSQEEQKQ

Parental  LEEDLLVEINRYALASHFFWGLWSILQASMSTIEFGYLE-YAQS-RFQFYFQQKGQLTSF
          LEE.LLVEIN.YAL..HF.WGL.SILQA.M.TI.FGY.E..AQS...QFYF.QKG.L.SF
Retrocopy LEEGLLVEINWYALVLHFYWGL*SILQAFMLTIVFGYFE<VAQS<LLQFYF*QKGHLISF

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_2344 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2344 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000011404	2 retrocopies	retro_rnor_1919, retro_rnor_1920,
Tupaia belangeri	ENSTBEG00000000172	1 retrocopy	retro_tbel_2344 ,