RetrogeneDB ID: retro_tbel_4408

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_81332:8625..8840(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf57
• Ensembl ID: ENSTBEG00000004344
• Aliases: None
• Description: chromosome 6 open reading frame 57 [Source:HGNC Symbol;Acc:20957]

Sequence

>retro_tbel_4408
TATGGCTGCGCCCTGGCCACAGCTAGGAGAGTGACAAGATCGCACCTTCTATGTCATTCCTTGAGGAAAACAAGTTCTCA
AGAAAGAAACCCTGAACCTGTCAAACAACCCCTTAAGAACCAAAGTTACCAAAAGGTCATTTTGATGTACCAGAGGATTC
CAATTTAGAGAAAAAACCACTAGAAAAATTTCCAGACGATGTTACCAAAGAAAAA

Alignment

ORF - retro_tbel_4408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 71.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FGRLPASARRAARSRPLYHSLRKTSSSQERNPEPVKQSLK-KPKLPEGRFDAPEDSNLEKEPLEKFPDDI
          .G...A.ARR..RS..L.HSLRKTSS.QERNPEPVKQ.LK..PKLP.G.FD.PEDSNLEK.PLEKFPDD.
Retrocopy YGCALATARRVTRSHLLCHSLRKTSS-QERNPEPVKQPLK<EPKLPKGHFDVPEDSNLEKKPLEKFPDD-

Parental  NPVTKEK
          ..VTKEK
Retrocopy --VTKEK

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_4408 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4408 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002602	2 retrocopies	retro_cfam_268, retro_cfam_657,
Choloepus hoffmanni	ENSCHOG00000011410	6 retrocopies	retro_chof_176, retro_chof_1854, retro_chof_252, retro_chof_465, retro_chof_694, retro_chof_966,
Erinaceus europaeus	ENSEEUG00000011260	1 retrocopy	retro_eeur_539,
Echinops telfairi	ENSETEG00000011154	1 retrocopy	retro_etel_1362,
Felis catus	ENSFCAG00000026799	1 retrocopy	retro_fcat_986,
Rattus norvegicus	ENSRNOG00000028087	1 retrocopy	retro_rnor_1514,
Tupaia belangeri	ENSTBEG00000004344	2 retrocopies	retro_tbel_3788, retro_tbel_4408 ,
Tarsius syrichta	ENSTSYG00000001769	1 retrocopy	retro_tsyr_67,