RetrogeneDB ID: retro_dord_785

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_97594:4688..4901(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2e1
• Ensembl ID: ENSDORG00000015441
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 1 [Source:MGI Symbol;Acc:MGI:107411]

Sequence

>retro_dord_785
GAGAAGGAGCTAGCCCAAATGTCCCTTGCTCCTCATGCTAACTGCATTGCTGACCCAAAAGGAGATGACATTTGTGAATG
AAGCAGCTATATTGATCCACCGGGTTCTGAGTGAGAAGTGATGTTTTGTTTGTTTTTTCCATCAGATTATCTGCTTAAAC
CACCAAAGGTTACTTTCCACACCAGAATCTACCACTGCAACAGCAGTCAAGAG

Alignment

ORF - retro_dord_785 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.0 %
• Parental protein coverage: 68.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHC
          .KELA...L.P..NC.A.PKGD.I.E..S....PPGS..E..V.F....F...Y..KPPKVTF.TRIYHC
Retrocopy EKELAQMSLAPHANCIADPKGDDICE*-SSYIDPPGSE*E--VMFC-LFFPSDYLLKPPKVTFHTRIYHC

Parental  NINSQ
          N....
Retrocopy NSSQE

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_785 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Dipodomys ordii	ENSDORG00000006762	2 retrocopies	retro_dord_172, retro_dord_323,
Dipodomys ordii	ENSDORG00000006888	5 retrocopies	retro_dord_104, retro_dord_345, retro_dord_408, retro_dord_743, retro_dord_760,
Dipodomys ordii	ENSDORG00000011406	1 retrocopy	retro_dord_357,
Dipodomys ordii	ENSDORG00000015441	1 retrocopy	retro_dord_785 ,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Pteropus vampyrus	ENSPVAG00000001773	1 retrocopy	retro_pvam_1451,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,
Ictidomys tridecemlineatus	ENSSTOG00000025799	2 retrocopies	retro_itri_1371, retro_itri_645,