RetrogeneDB ID: retro_dord_353

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_13462:16990..17665(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Grpel2
• Ensembl ID: ENSDORG00000011142
• Aliases: None
• Description: GrpE-like 2, mitochondrial [Source:MGI Symbol;Acc:MGI:1334416]

Sequence

>retro_dord_353
ATGACCTCGAGGTCGCTGTGGGCGGTCCGGCGGCGGGTGCAGCGCCTCCTGGCCTCCAGCATCCTGCCTGATAGCAGGGA
ATGGCTGCCCCCATTCAGTACTGCCACACAGAGAAATGCTGGTGAGGACTGCAGTTCTGAGGACCCTCCTGTTGACCATG
GGCCCTCTCTTGCTGAACAAGCCTTAAGGTTAAAAGCTGTTAAACTGGAGAAGGAAGTCCAGGATTTGACATTGAGGTAC
CAGAGAGCTGTAGCTGATTGCAAAAACATAAGGAGACGAACCCAGAGATGTGTGGAAGACGCCAAGATATTTGGAATCCA
GAGCTTCTGTAAAGATTTGGTGGAGGTGGCAGACATCTTGGAGAACACTACTAAGTGCATTTCTGAAGAAGTAGACCCTG
AGGACCAGAAGCTCACTCTGGAGAAAGTCTTCCGAGGGTTGTCACTTTTAGAAGCTAAGCTGAAAAGTGTGTTTACCAAG
CATGGCCTGGAAAAGATGGCACCCATTGGTGACAAATATGACCCTCATGAGCATGAACTCATCTGTCACATTCCAGCTGG
TATTGGCGTGCAGCCTTGCACTGTGGCATTAGTAAGGCATGATGGGTACAAACTTCATGGTCGCACCATTAGACTGGCCC
AGGTGGAAGTGGCTGTTGAGTCTCAGAGAAGACTT

Alignment

ORF - retro_dord_353 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAARSLWAVRRRVQRLLASCIPPDSREWLPPFSTATQRNAGEDCSSEDPPVDRGPSLAEQALRLKAVKLE
          M..RSLWAVRRRVQRLLAS.I.PDSREWLPPFSTATQRNAGEDCSSEDPPVD.GPSLAEQALRLKAVKLE
Retrocopy MTSRSLWAVRRRVQRLLASSILPDSREWLPPFSTATQRNAGEDCSSEDPPVDHGPSLAEQALRLKAVKLE

Parental  KEVQDLTLRYQRAVADCENIRRRTQRCVEDAKIFGIQSFCKDLVEVADILENTTKCISEEVDPEDQKLTL
          KEVQDLTLRYQRAVADC.NIRRRTQRCVEDAKIFGIQSFCKDLVEVADILENTTKCISEEVDPEDQKLTL
Retrocopy KEVQDLTLRYQRAVADCKNIRRRTQRCVEDAKIFGIQSFCKDLVEVADILENTTKCISEEVDPEDQKLTL

Parental  EKVFRGLSLLEAKLKSVFTKHGLEKMAPIGDKYDPHEHELICHVPAGIGVQPGTVALVRHDGYKLHGRTI
          EKVFRGLSLLEAKLKSVFTKHGLEKMAPIGDKYDPHEHELICH.PAGIGVQP.TVALVRHDGYKLHGRTI
Retrocopy EKVFRGLSLLEAKLKSVFTKHGLEKMAPIGDKYDPHEHELICHIPAGIGVQPCTVALVRHDGYKLHGRTI

Parental  RLAQVEVAVESQRRL
          RLAQVEVAVESQRRL
Retrocopy RLAQVEVAVESQRRL

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_353 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004070	1 retrocopy	retro_chof_1984,
Dipodomys ordii	ENSDORG00000011142	1 retrocopy	retro_dord_353 ,
Felis catus	ENSFCAG00000003624	1 retrocopy	retro_fcat_618,
Homo sapiens	ENSG00000164284	2 retrocopies	retro_hsap_1284, retro_hsap_4842,
Gorilla gorilla	ENSGGOG00000005410	2 retrocopies	retro_ggor_1008, retro_ggor_3021,
Macaca mulatta	ENSMMUG00000021662	1 retrocopy	retro_mmul_1317,
Nomascus leucogenys	ENSNLEG00000010160	1 retrocopy	retro_nleu_710,
Oryctolagus cuniculus	ENSOCUG00000016138	3 retrocopies	retro_ocun_89, retro_ocun_905, retro_ocun_943,
Otolemur garnettii	ENSOGAG00000014326	1 retrocopy	retro_ogar_791,
Pongo abelii	ENSPPYG00000015933	2 retrocopies	retro_pabe_1063, retro_pabe_3764,
Pan troglodytes	ENSPTRG00000017396	2 retrocopies	retro_ptro_3226, retro_ptro_877,
Sorex araneus	ENSSARG00000005467	2 retrocopies	retro_sara_320, retro_sara_511,