RetrogeneDB ID: retro_dord_480

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_22055:15175..15405(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl13
• Ensembl ID: ENSDORG00000016654
• Aliases: None
• Description: mitochondrial ribosomal protein L13 [Source:MGI Symbol;Acc:MGI:2137218]

Sequence

>retro_dord_480
GACTGTGGAGACCATGTTGTCATAATGACCACAAAGCATACTGCATTTTCTGGAAACAAATGAGAACAAAAAGTATATTC
CTCTTATACTGGCTACTCTGGTGGATTTAAACAAGTAACAGCTGCTCAGCTTCACCAGAGGGCTCCAGTGGCAATTGTGA
AATTGGCTATTTATGGCATGCTGCCAAAAACCTTCACAGGAGAACAATGATGCAAAGGCTACCTCTTTTC

Alignment

ORF - retro_dord_480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.46 %
• Parental protein coverage: 60.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DCGDHVVIMNTRHIAFSGNKWEQKVYSSHTGYPGGFKQVTAAQLHQRDPVAIVKLAIYGMLPK-NLHRRT
          DCGDHVVIM.T.H.AFSGNK.EQKVYSS.TGY.GGFKQVTAAQLHQR.PVAIVKLAIYGMLPK.NLHRRT
Retrocopy DCGDHVVIMTTKHTAFSGNK*EQKVYSSYTGYSGGFKQVTAAQLHQRAPVAIVKLAIYGMLPK<NLHRRT

Parental  MMQRLHLF
          MMQRL.LF
Retrocopy MMQRLPLF

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_480 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	ENSCHOG00000006926	1 retrocopy	retro_chof_648,
Callithrix jacchus	ENSCJAG00000005359	1 retrocopy	retro_cjac_162,
Dipodomys ordii	ENSDORG00000016654	1 retrocopy	retro_dord_480 ,
Equus caballus	ENSECAG00000021161	1 retrocopy	retro_ecab_952,
Mustela putorius furo	ENSMPUG00000001080	2 retrocopies	retro_mputfur_1585, retro_mputfur_623,
Oryctolagus cuniculus	ENSOCUG00000016189	1 retrocopy	retro_ocun_675,
Ochotona princeps	ENSOPRG00000015721	2 retrocopies	retro_opri_274, retro_opri_454,
Pteropus vampyrus	ENSPVAG00000003719	1 retrocopy	retro_pvam_627,
Rattus norvegicus	ENSRNOG00000004401	1 retrocopy	retro_rnor_2720,
Sus scrofa	ENSSSCG00000005996	1 retrocopy	retro_sscr_1183,
Tupaia belangeri	ENSTBEG00000004571	5 retrocopies	retro_tbel_1026, retro_tbel_1596, retro_tbel_2517, retro_tbel_3095, retro_tbel_456,