RetrogeneDB ID: retro_dord_155

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4018:401412..401732(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufa7
• Ensembl ID: ENSDORG00000012324
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (B14.5a) [Source:MGI Symbol;Acc:MGI:1913666]

Sequence

>retro_dord_155
ACCATTATTCAGAGACTGAGGAACTGGGCATCCCGGCTAAACCTGCAGGTGATGCTGCAGCTGCGCTACCAGGAGATCGC
CAAGTGGACTCAGCTGCCTCCCAAGCTCTGGGGGCCCAGCCACAAGCTCTCCAACAATCACTATTGCCCTCCTGATGGCC
GCCGGGAAGTCTTACCCCCATCCATTATCTGACCGCCCAGAAGATGCTGGTGGCAGGCAAAATGGCAGAGAGCTCCGAGG
CTGAAGCCACAGAGAAGAAGGCCATAACCCATGCTCCTCCTGTGAAGAAGTGGGAGCTATCCAGGGACCAGTCTTACCTG

Alignment

ORF - retro_dord_155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.06 %
• Parental protein coverage: 95.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TIIQRLRNWASGQNLQAKLQLRYQEIAKRTQPPPKLPVGPSHKLSNNYYCTRDGRREVVPPSIV-MTSQK
          TIIQRLRNWAS..NLQ..LQLRYQEIAK.TQ.PPKL..GPSHKLSNN.YC..DGRREV.PPSI...T.QK
Retrocopy TIIQRLRNWASRLNLQVMLQLRYQEIAKWTQLPPKL-WGPSHKLSNNHYCPPDGRREVLPPSII<LTAQK

Parental  VLVAGKTAASSEVEATEKKAITPAPPMKRWELSKDQPYL
          .LVAGK.A.SSE.EATEKKAIT.APP.K.WELS.DQ.YL
Retrocopy MLVAGKMAESSEAEATEKKAITHAPPVKKWELSRDQSYL

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_155 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000685	1 retrocopy	retro_chof_2004,
Callithrix jacchus	ENSCJAG00000010709	2 retrocopies	retro_cjac_2942, retro_cjac_956,
Dipodomys ordii	ENSDORG00000012324	1 retrocopy	retro_dord_155 ,
Macropus eugenii	ENSMEUG00000015637	3 retrocopies	retro_meug_1487, retro_meug_149, retro_meug_587,
Rattus norvegicus	ENSRNOG00000006939	2 retrocopies	retro_rnor_1491, retro_rnor_1793,