RetrogeneDB ID: retro_tbel_293

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1670:112778..113164(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHTOP
• Ensembl ID: ENSTBEG00000012442
• Aliases: None
• Description: chromatin target of PRMT1 [Source:HGNC Symbol;Acc:24511]

Sequence

>retro_tbel_293
GGACATGCCACCAGAACCCTCCTTAGGGGCAGGATGTCACTCCAAGGTCAAAACCTGCTCCGAGGTGGATGAGCCGTAGC
TCCCTGAATGGGCTTAAGAAGAGGTGGTGTTCGAGGTCGTGGAGGTCCTGGGAGAGGGGGCCTAGGGCGTGGAGCTAAGG
GTGGTGGCCGAATCGGTGGTAGAGGTCGGGGTATGATAGGTCGGGGAAGAGGGGGCTTTGGAGGCAGAGGCAGAGGCGGT
GGACGAGGAAGAGGTGCCCTGACTCGCCCTGTATTGACCAAGGAGCAGCTGGACAACCAGTTGGATGCATACATGTCGAA
AACGAAAGGACACCTGGAAGCTGAGTTAGATGCTACATGGCACAGACAGATCCCGAAACCAGCGAC

Alignment

ORF - retro_tbel_293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.46 %
• Parental protein coverage: 51.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRATRTLLRGGMSLRGQNLLRGGRAVAP-RGLRRGGVRGRG-PGRG-LGRGAMGRG-IGGRGRGMIGRGR
          G.ATRTLLRG.MSL.GQNLLRGG.AVAP..GLRRGGVRGRG.PGRG.LGRGA.G.G.IGGRGRGMIGRGR
Retrocopy GHATRTLLRGRMSLQGQNLLRGG*AVAP*MGLRRGGVRGRGGPGRGGLGRGAKGGGRIGGRGRGMIGRGR

Parental  GGFGGRGRGRGRGRGALTRPVLTKEQLDNQLDAYMSKTKGHLDAELDA-YMAQTDPETND
          GGFGGRGRG.GRGRGALTRPVLTKEQLDNQLDAYMSKTKGHL.AELDA.YMAQTDPET.D
Retrocopy GGFGGRGRGGGRGRGALTRPVLTKEQLDNQLDAYMSKTKGHLEAELDA<YMAQTDPETSD

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_293 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_293 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Callithrix jacchus	ENSCJAG00000010383	3 retrocopies	retro_cjac_2059, retro_cjac_423, retro_cjac_431,
Felis catus	ENSFCAG00000002740	1 retrocopy	retro_fcat_1925,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Mus musculus	ENSMUSG00000001017	2 retrocopies	retro_mmus_1693, retro_mmus_1852,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Ictidomys tridecemlineatus	ENSSTOG00000000660	1 retrocopy	retro_itri_1169,
Tupaia belangeri	ENSTBEG00000012442	1 retrocopy	retro_tbel_293 ,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,