RetrogeneDB ID: retro_dord_167

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4246:52581..52827(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dph3
• Ensembl ID: ENSDORG00000011642
• Aliases: None
• Description: DPH3 homolog (KTI11, S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1922658]

Sequence

>retro_dord_167
ATGGCGGTATTTCACGACGAGGTGGAGATCGAAGACTTCCAGTATGATGAGGACTTGGAAACCTATTTCTACCCCTGCCC
ATGTGGCGATAAATTCTCTATCACCAAAGAAGATTTGGAGAATGGGGAAGAGGTGGCAACGTGTCCTAGCTGTTCTCTTA
TTATAAAAGTAATTTATGACAAAGATCAGTTTATGTGTGGAGAAACAATCCCAGCTCCTTCAGCCAACAAAGAATTAGTT
AAATGC

Alignment

ORF - retro_dord_167 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVFHDEVEIEDFQYDEDSETFFYPCPCGDNFSITKEDLENGEEVATCPSCSLIIKVIYDKDQFMCGETI
          MAVFHDEVEIEDFQYDED.ET.FYPCPCGD.FSITKEDLENGEEVATCPSCSLIIKVIYDKDQFMCGETI
Retrocopy MAVFHDEVEIEDFQYDEDLETYFYPCPCGDKFSITKEDLENGEEVATCPSCSLIIKVIYDKDQFMCGETI

Parental  PAPSANKELVKC
          PAPSANKELVKC
Retrocopy PAPSANKELVKC

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_167 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012030	1 retrocopy	retro_dnov_39,
Dipodomys ordii	ENSDORG00000011642	1 retrocopy	retro_dord_167 ,
Erinaceus europaeus	ENSEEUG00000009790	1 retrocopy	retro_eeur_502,
Echinops telfairi	ENSETEG00000016272	1 retrocopy	retro_etel_1879,
Homo sapiens	ENSG00000154813	1 retrocopy	retro_hsap_2438,
Gorilla gorilla	ENSGGOG00000022108	1 retrocopy	retro_ggor_174,
Loxodonta africana	ENSLAFG00000025650	3 retrocopies	retro_lafr_31, retro_lafr_545, retro_lafr_87,
Macaca mulatta	ENSMMUG00000022692	2 retrocopies	retro_mmul_2085, retro_mmul_497,
Monodelphis domestica	ENSMODG00000025472	3 retrocopies	retro_mdom_131, retro_mdom_1434, retro_mdom_609,
Mus musculus	ENSMUSG00000021905	1 retrocopy	retro_mmus_196,
Nomascus leucogenys	ENSNLEG00000001096	2 retrocopies	retro_nleu_2876, retro_nleu_2913,
Pongo abelii	ENSPPYG00000014083	1 retrocopy	retro_pabe_1795,
Pan troglodytes	ENSPTRG00000014671	1 retrocopy	retro_ptro_1409,
Tupaia belangeri	ENSTBEG00000011675	1 retrocopy	retro_tbel_58,
Tursiops truncatus	ENSTTRG00000007739	3 retrocopies	retro_ttru_1474, retro_ttru_31, retro_ttru_907,