RetrogeneDB ID: retro_dord_306

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_10897:23723..24112(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2r2
• Ensembl ID: ENSDORG00000007589
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2R 2 [Source:MGI Symbol;Acc:MGI:1914865]

Sequence

>retro_dord_306
CCCAACATTTATGAGAATGGTGATTATACATTTCAATTCTTCATCCACCTGCAGAAGACCCATACTGTGGAGAACTCCCC
TCAGAAAGGTGGAGTCCTCCTCAGAATATGAGAACTATCAGTGTAATCTCAATGTTTAACGAGCCCAAGACCTTCTCCCC
AGTCAACGTGGATACTCCTGTTATATTCAGGAAATGGGGGGACAGCAAAGAAAAAGACAAAGAATGTGCTGAAATCGTTA
GGAAACAGGTTTCAGCCACCAAGGCTGAAGAAGATGAAGTGAAGGTCCCTACAACTCTGGTAGAATACTGAATCAAACCT
AAAGTGTCTTCCAATGCCAATTACATTTTTCTTAGTTCAGATTTGCTTGAAGATGAATTGTATAATGAT

Alignment

ORF - retro_dord_306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.11 %
• Parental protein coverage: 54.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PNIYENGD-VCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPANVDASVMFRKWR
          PNIYENGD...ISILHPP..DP..GELPSERW.P.QN.RTI..SVIS..NEP.TFSP.NVD..V.FRKW.
Retrocopy PNIYENGD<LYISILHPPAEDPYCGELPSERWSPPQNMRTI--SVISMFNEPKTFSPVNVDTPVIFRKWG

Parental  DSKGKDKEYAEIIRKQVSATKAEAEKDGVKVPTTLAEYCIKTKVPSNDN----SSDLLYDDLYDD
          DSK.KDKE.AEI.RKQVSATKAE...D.VKVPTTL.EY.IK.KV.SN.N....SSDLL.D.LY.D
Retrocopy DSKEKDKECAEIVRKQVSATKAE--EDEVKVPTTLVEY*IKPKVSSNANYIFLSSDLLEDELYND

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_306 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031810	1 retrocopy	retro_cfam_1138,
Dipodomys ordii	ENSDORG00000007589	1 retrocopy	retro_dord_306 ,
Myotis lucifugus	ENSMLUG00000006793	1 retrocopy	retro_mluc_2175,
Oryctolagus cuniculus	ENSOCUG00000023588	3 retrocopies	retro_ocun_131, retro_ocun_1719, retro_ocun_1793,
Otolemur garnettii	ENSOGAG00000029045	3 retrocopies	retro_ogar_1211, retro_ogar_2040, retro_ogar_2946,
Rattus norvegicus	ENSRNOG00000010727	1 retrocopy	retro_rnor_1508,