RetrogeneDB ID: retro_dord_613

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_40620:4250..4518(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmb6
• Ensembl ID: ENSDORG00000005851
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type 6 [Source:MGI Symbol;Acc:MGI:104880]

Sequence

>retro_dord_613
ATGGCAGCCACCTTAGTAAGTGTAGGAGGAATTGGCCCTTCCCCCAGAATGGGGACCCGAGGCCATTGCTCCTGACTGGG
AAAACAGGGTAGTGACCACAGGGACCACCATCATGGCTGTGCAGTTTGGCAGGGGTGTGGTTCTAGGGGCTGACTCCAGG
GGGTCCTACATCCCAAAGCCAGTGATGGACAAGCTGACCCCTATTCACGACCGAATTTTCTGCTGTTGCTCAGGCTTAGC
AGCTGATACCCAAGCAGCAGCGGATGCT

Alignment

ORF - retro_dord_613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.49 %
• Parental protein coverage: 64.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAATLVTAAGMGPAPA-WGPEAIAPDWENREVTTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLT
          MAATLV...G.GP.P..WGPEAIAPDWENR.VTTGTTIMAVQF..GVVLGADSR...GSYI...V.DKLT
Retrocopy MAATLVSVGGIGPSPR>WGPEAIAPDWENRVVTTGTTIMAVQFGRGVVLGADSR---GSYIPKPVMDKLT

Parental  PIHDRIFCCRSGSAADTQAVADA
          PIHDRIFCC.SG.AADTQA.ADA
Retrocopy PIHDRIFCCCSGLAADTQAAADA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_613 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000005851	1 retrocopy	retro_dord_613 ,
Erinaceus europaeus	ENSEEUG00000002083	3 retrocopies	retro_eeur_203, retro_eeur_607, retro_eeur_71,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Vicugna pacos	ENSVPAG00000000595	1 retrocopy	retro_vpac_400,