RetrogeneDB ID: retro_dord_741

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_70206:1713..2254(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000007597
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl18
• Ensembl ID: ENSDORG00000011514
• Aliases: None
• Description: mitochondrial ribosomal protein L18 [Source:MGI Symbol;Acc:MGI:1914931]

Sequence

>retro_dord_741
ATGGTGCTTGAGCTGCGGCTCTGGAAATTGTCTTTGGCTTGCAGGAGCCTAAAGCGGGCCTGCGCCGCCCTCTCCAGCTC
CACGCCGGCCGGCCGTGAGCCCTGCCGAGCAGCCTTCGGAAAACGAAGCCGTGGCTCCCGAGTTCACCAACAGGAATCCC
CGGAACCTGGAGCTCTTGGCAGTGGCCAGGAAGGAACGAGGTTGGAGGACCGTGTGGCTCTCGCGGGAGTTCTGGCACAG
GTTACGAGTTATAAGGACTCAGCATCACGTAGAAGGGATTGTTGAGCATCGAAATGGCCAGGTTGTGGTTTCAGCATCCA
CCCGGGAATGGGCTATTAAAAAGCACCTTTACAGCACCAAAAATGTGGTGGCTTGTGAGAGTATAGGACGAGTGCTGGCC
CAGCGTTGCTTGGAGGCAGGCATCAACTTCATGGTCTACCAACCAACCCCATGGGAGGCAGCCTCAGATTCGATGAAACG
CCTACAGAATGCCATGACAGAAGGTGGTGTGGTACTGAAGGAGCCTCGGAGAATCTATGAG

Alignment

ORF - retro_dord_741 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALQLRLWKLPSACRSLERACAALS-STT-PAVSPAEQPSENEAVAPEFTNRNPRNLELLAVARKERGWR
          M.L.LRLWKL..ACRSL.RACAALS.ST..PAVSPAEQPSENEAVAPEFTNRNPRNLELLAVARKERGWR
Retrocopy MVLELRLWKLSLACRSLKRACAALSSSTP>PAVSPAEQPSENEAVAPEFTNRNPRNLELLAVARKERGWR

Parental  TVWPSREFWHRLRVIRTQHHVEGIVEHQNGQVVVSASTREWAIKKHLYSTKNVVACESIGRVLAQRCLEA
          TVW.SREFWHRLRVIRTQHHVEGIVEH.NGQVVVSASTREWAIKKHLYSTKNVVACESIGRVLAQRCLEA
Retrocopy TVWLSREFWHRLRVIRTQHHVEGIVEHRNGQVVVSASTREWAIKKHLYSTKNVVACESIGRVLAQRCLEA

Parental  GINFMVYQPTPWEAASDSMKRLQNAMTEGGVVLKEPRRIYE
          GINFMVYQPTPWEAASDSMKRLQNAMTEGGVVLKEPRRIYE
Retrocopy GINFMVYQPTPWEAASDSMKRLQNAMTEGGVVLKEPRRIYE

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_741 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015398	1 retrocopy	retro_amel_1445,
Dipodomys ordii	ENSDORG00000011514	1 retrocopy	retro_dord_741 ,
Echinops telfairi	ENSETEG00000007591	1 retrocopy	retro_etel_438,
Homo sapiens	ENSG00000112110	1 retrocopy	retro_hsap_1664,
Gorilla gorilla	ENSGGOG00000014075	1 retrocopy	retro_ggor_1255,
Macaca mulatta	ENSMMUG00000017037	1 retrocopy	retro_mmul_61,
Mus musculus	ENSMUSG00000057388	1 retrocopy	retro_mmus_1940,
Otolemur garnettii	ENSOGAG00000007327	1 retrocopy	retro_ogar_1660,
Pongo abelii	ENSPPYG00000017147	3 retrocopies	retro_pabe_1416, retro_pabe_1418, retro_pabe_1421,
Pan troglodytes	ENSPTRG00000018761	1 retrocopy	retro_ptro_1128,
Pteropus vampyrus	ENSPVAG00000005322	2 retrocopies	retro_pvam_1480, retro_pvam_252,
Tarsius syrichta	ENSTSYG00000005598	1 retrocopy	retro_tsyr_1847,