RetrogeneDB ID: retro_dord_172

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4441:4808..5225(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2d3
• Ensembl ID: ENSDORG00000006762
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 3 [Source:MGI Symbol;Acc:MGI:1913355]

Sequence

>retro_dord_172
GAACTTAGTGATTTGGCCCAGGGCCCTCCTGCACAGTGCTCTGCAGGTCCAGTTGGGGATGACATGTTTCACTGGCAAGC
CACAATTATAGGACCTAATGACAGCCCATCTCAAGGCGGTGTATTCCTTGTGACAATTCATTTTCCTACAGACTACCCCT
TCAAACCACCTAAGGTTGCATTTACAACAAGAATTTACCATCCAAGTATCAACAGTAATGGCAGCATTTGTCTTGATATT
CTAAGGTCACAGTGGTCTCCTGCTTTAACGGTTTCTAAAGTTCTTTTATCCAGTTGTTCACTGCTATGTGATCCGACCCC
AGATGACCCCCTTGTGCCAGAGATTGCACAGATCTATAAAACAGACAGAGATAAGTACAACAGAATATCTCGGGAATGGA
CTCAGAAGTATGCCATG

Alignment

ORF - retro_dord_172 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNI
          ELSDLA..PPAQCSAGPVGDDMFHWQATI.GPNDSP.QGGVF..TIHFPTDYPFKPPKVAFTTRIYHP.I
Retrocopy ELSDLAQGPPAQCSAGPVGDDMFHWQATIIGPNDSPSQGGVFLVTIHFPTDYPFKPPKVAFTTRIYHPSI

Parental  NSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM
          NSNGSICLDILRSQWSPALT.SKVLLS.CSLLCDP.PDDPLVPEIA.IYKTDRDKYNRISREWTQKYAM
Retrocopy NSNGSICLDILRSQWSPALTVSKVLLSSCSLLCDPTPDDPLVPEIAQIYKTDRDKYNRISREWTQKYAM

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_172 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 20 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004649	2 retrocopies	retro_chof_2549, retro_chof_439,
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Callithrix jacchus	ENSCJAG00000015492	3 retrocopies	retro_cjac_512, retro_cjac_657, retro_cjac_791,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
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,
Equus caballus	ENSECAG00000020678	1 retrocopy	retro_ecab_859,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Gorilla gorilla	ENSGGOG00000010832	1 retrocopy	retro_ggor_953,
Macropus eugenii	ENSMEUG00000004256	6 retrocopies	retro_meug_1034, retro_meug_1503, retro_meug_2138, retro_meug_564, retro_meug_787, retro_meug_89,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,