RetrogeneDB ID: retro_dord_196

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_5125:9733..10086(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl49
• Ensembl ID: ENSDORG00000003613
• Aliases: None
• Description: mitochondrial ribosomal protein L49 [Source:MGI Symbol;Acc:MGI:108180]

Sequence

>retro_dord_196
ATGGCTGCGGCCATGGCCAGGTCTGTGCTGTGAGTCTGGAGAAGAACCGATATCCTGCGAGGCTGCGGACTAAGGCAGCT
GAGCCAGACCCAGAGGCCTCCTGATTACCCCAGCTTTATGGAGTCTGCAGATGAGAACTGGTTTGTCGAGCGCCTCTTAC
CCGCTACCAGCATCCCAAAGCCCCCCAAACATAACATTATCCCACGCCTAGTGGCTGGCAGCCTCCCAGAGACCCCCCAC
CCAACCTGCCCTATTTTGTGCGGCACTCCTGGATGTACAACATTCCTGTCTACTGGGACATCACACATGGCAATCTCCAG
ATGACTGTGATCCGGAAGGTGGAAAAGGACATC

Alignment

ORF - retro_dord_196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.99 %
• Parental protein coverage: 70.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAMVRSVLWVWRRTDIQRGCGLRQLSQ--KPRDYPSFVESADEYRCVERLIPSTNIPQPPKHE-HYPT
          MAAAM.RSVL.VWRRTDI.RGCGLRQLSQ...P.DYPSF.ESADE...VERL.P.T.IP.PPKH..HYPT
Retrocopy MAAAMARSVL*VWRRTDILRGCGLRQLSQTQRPPDYPSFMESADENWFVERLLPATSIPKPPKHN<HYPT

Parental  HSVWQPPRDPPPNLPYVVRRSRMYNIPVYRDITHGNRQMTVIRKVEGDI
          .S.WQPPRDPPPNLPY.VR.S.MYNIPVY.DITHGN.QMTVIRKVE.DI
Retrocopy PSGWQPPRDPPPNLPYFVRHSWMYNIPVYWDITHGNLQMTVIRKVEKDI

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_196 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012855	1 retrocopy	retro_chof_1006,
Dasypus novemcinctus	ENSDNOG00000004494	6 retrocopies	retro_dnov_1396, retro_dnov_1488, retro_dnov_1941, retro_dnov_2272, retro_dnov_2473, retro_dnov_2686,
Dipodomys ordii	ENSDORG00000003613	1 retrocopy	retro_dord_196 ,
Homo sapiens	ENSG00000149792	1 retrocopy	retro_hsap_3180,
Macropus eugenii	ENSMEUG00000009437	1 retrocopy	retro_meug_1151,
Microcebus murinus	ENSMICG00000016604	1 retrocopy	retro_mmur_629,
Macaca mulatta	ENSMMUG00000018778	1 retrocopy	retro_mmul_2031,
Nomascus leucogenys	ENSNLEG00000005505	1 retrocopy	retro_nleu_1659,
Oryctolagus cuniculus	ENSOCUG00000014882	1 retrocopy	retro_ocun_316,
Pan troglodytes	ENSPTRG00000003867	1 retrocopy	retro_ptro_2263,
Tupaia belangeri	ENSTBEG00000007929	2 retrocopies	retro_tbel_1350, retro_tbel_3334,