RetrogeneDB ID: retro_dord_237

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6298:19341..19630(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Commd6
• Ensembl ID: ENSDORG00000011048
• Aliases: None
• Description: COMM domain containing 6 [Source:MGI Symbol;Acc:MGI:1913450]

Sequence

>retro_dord_237
AGGCACCATGGAGGCGCCATGCCCTTTGCCATGGAGGAGTCTGGGGGGCAGAGAGCCATTAGATGCTAAGTCCAAAGCCA
CCAGCTAGCTTATAGATTTTCAATGGAAACTCGGTATGGCTGTGAGCTCAGACAGCTGTAGATCACTTAAGTATCCTTAT
GTTGTAGTAATGCTAAAAGTGGCAGATCATTCTGGCCAAGTAAAGAACAAGTCCTTTGAAATGACAATTCCTCAGTTTCA
GAATTTTTACAGATAGTTCAAGGAAATTGCTGCTGTTTTTGAAACTGTG

Alignment

ORF - retro_dord_237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.65 %
• Parental protein coverage: 76.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPRRGSRALSMEETGG-REPVLDAKSEVTSQLIDFQWKLGMAVSSDSCRSLKYPYVAVMLKVADHSGQVK
          R...G.....MEE.GG.REP.LDAKS..TS.LIDFQWKLGMAVSSDSCRSLKYPYV.VMLKVADHSGQVK
Retrocopy RHHGGAMPFAMEESGG>REP-LDAKSKATS*LIDFQWKLGMAVSSDSCRSLKYPYVVVMLKVADHSGQVK

Parental  NKSFEMTIPQFQNFYRQFKEIAAVIETV
          NKSFEMTIPQFQNFYR.FKEIAAV.ETV
Retrocopy NKSFEMTIPQFQNFYR*FKEIAAVFETV

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_237 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011048	1 retrocopy	retro_dord_237 ,
Erinaceus europaeus	ENSEEUG00000006061	2 retrocopies	retro_eeur_120, retro_eeur_560,
Myotis lucifugus	ENSMLUG00000010697	1 retrocopy	retro_mluc_1927,
Monodelphis domestica	ENSMODG00000000970	3 retrocopies	retro_mdom_111, retro_mdom_147, retro_mdom_76,
Nomascus leucogenys	ENSNLEG00000026952	1 retrocopy	retro_nleu_2240,
Rattus norvegicus	ENSRNOG00000038012	1 retrocopy	retro_rnor_2012,
Tursiops truncatus	ENSTTRG00000003379	2 retrocopies	retro_ttru_1697, retro_ttru_908,