RetrogeneDB ID: retro_dord_180

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4703:38132..38453(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cox11
• Ensembl ID: ENSDORG00000001207
• Aliases: None
• Description: cytochrome c oxidase assembly protein 11 [Source:MGI Symbol;Acc:MGI:1917052]

Sequence

>retro_dord_180
ACTACAGGACTTGGTGGATCAGCAGTAGCAGGGCATGCATCAGACCAGATTGAAAACATGGTGCCTGTTAAGGACTGGAT
CATTAAGGTGATCTTCAATGCAGACGTGCATGCCAGTTGCCAGTGGAACTTCAGACCTCAGCAAGCAGAAATATATGTGG
TACCAGGAGAGACTGCACTAGCATTTTACAAAGCTAAGAATCCTACCGACAAACCAATAATTGGAATTTCTACATACAAT
GTTGTACCATTTGAAGCTGGGCAGTATTTCAATAAAATTCAGTGCTTCTGTTTTGAAGAACAAAGGCCTAATCCCCAAGA
A

Alignment

ORF - retro_dord_180 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.33 %
• Parental protein coverage: 69.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTGLGGSAVAGHASDQIENMVPVKDRIIKVTFNADVHASLQWNFRPQQTEIYVVPGETALAFYKAKNPTD
          TTGLGGSAVAGHASDQIENMVPVKD.IIKV.FNADVHAS.QWNFRPQQ.EIYVVPGETALAFYKAKNPTD
Retrocopy TTGLGGSAVAGHASDQIENMVPVKDWIIKVIFNADVHASCQWNFRPQQAEIYVVPGETALAFYKAKNPTD

Parental  KPIIGISTYNVVPFEAGQYFNKIQCFCFEEQRLNPQE
          KPIIGISTYNVVPFEAGQYFNKIQCFCFEEQR.NPQE
Retrocopy KPIIGISTYNVVPFEAGQYFNKIQCFCFEEQRPNPQE

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_180 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008482	1 retrocopy	retro_cpor_1340,
Dasypus novemcinctus	ENSDNOG00000014862	1 retrocopy	retro_dnov_1933,
Dipodomys ordii	ENSDORG00000001207	1 retrocopy	retro_dord_180 ,
Homo sapiens	ENSG00000166260	1 retrocopy	retro_hsap_3442,
Microcebus murinus	ENSMICG00000005225	1 retrocopy	retro_mmur_1119,
Monodelphis domestica	ENSMODG00000014855	1 retrocopy	retro_mdom_952,
Mus musculus	ENSMUSG00000020544	4 retrocopies	retro_mmus_1318, retro_mmus_2318, retro_mmus_2714, retro_mmus_986,
Nomascus leucogenys	ENSNLEG00000007990	1 retrocopy	retro_nleu_2297,
Ochotona princeps	ENSOPRG00000004138	1 retrocopy	retro_opri_441,
Pongo abelii	ENSPPYG00000008259	2 retrocopies	retro_pabe_156, retro_pabe_2847,
Pan troglodytes	ENSPTRG00000009422	1 retrocopy	retro_ptro_2335,
Rattus norvegicus	ENSRNOG00000046318	1 retrocopy	retro_rnor_1515,