RetrogeneDB ID: retro_dord_412

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_172521:211..567(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrps10
• Ensembl ID: ENSDORG00000002081
• Aliases: None
• Description: mitochondrial ribosomal protein S10 [Source:MGI Symbol;Acc:MGI:1928139]

Sequence

>retro_dord_412
TATATAAATACGTCAATCTTAGTAAAAGGCCATGATAAGGATGTATTGACAGTTATGAATATTTTGCTGTGTTAGCTGCT
AAAAAACTTGGTATTTCTATTAAAGTACATGAACCTCCAAGGAAAACAGAGTGATTTACTCTTCTCAAATCAGTGCATGT
TTTTAAGACGCACAGAGTTCAATATGAAATGAGAATACTTTATGGATGTTTGGAGTTATAACAACTCACTGGATGCACAG
CCGATGTCTACTTGGAATACATTCAGTGAAACTTACCTGAAGGGGTCGCCATGGAAGTAACAAAGACACAATTAGAACAG
TTACCAGAACACATCAAAAAGCCAATCTAGGAAACA

Alignment

ORF - retro_dord_412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.17 %
• Parental protein coverage: 63.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YKRLSILVKGHDKAVL-DSYEYFAVLAAKELGISIKVHEPPRKIERFTLLKSVHIFKKHRVQYEMRTLYR
          Y...SILVKGHDK.VL.DSYEYFAVLAAK.LGISIKVHEPPRK.E.FTLLKSVH.FK.HRVQYEMR.LY.
Retrocopy YINTSILVKGHDKDVL<DSYEYFAVLAAKKLGISIKVHEPPRKTE*FTLLKSVHVFKTHRVQYEMRILYG

Parental  CLELKHLTGCTANVYLEYIQRNLPEGVAMEVTKTHLEQLLEHIKKPIWET
          CLEL..LTGCTA.VYLEYIQ.NLPEGVAMEVTKT.LEQL.EHIKKPI.ET
Retrocopy CLEL*QLTGCTADVYLEYIQ*NLPEGVAMEVTKTQLEQLPEHIKKPI*ET

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_412 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000002081	1 retrocopy	retro_dord_412 ,
Homo sapiens	ENSG00000048544	1 retrocopy	retro_hsap_4157,
Gorilla gorilla	ENSGGOG00000012808	1 retrocopy	retro_ggor_2532,
Microcebus murinus	ENSMICG00000011379	1 retrocopy	retro_mmur_321,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Oryctolagus cuniculus	ENSOCUG00000016697	1 retrocopy	retro_ocun_1141,
Pongo abelii	ENSPPYG00000016613	1 retrocopy	retro_pabe_3456,
Pan troglodytes	ENSPTRG00000018169	1 retrocopy	retro_ptro_2826,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284,
Ictidomys tridecemlineatus	ENSSTOG00000027016	1 retrocopy	retro_itri_1183,