RetrogeneDB ID: retro_dord_104

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_326:119605..119853(-)
• Located in intron of: ENSDORG00000016124

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2d4
• Ensembl ID: ENSDORG00000006888
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 4 [Source:MGI Symbol;Acc:MGI:3644823]

Sequence

>retro_dord_104
TTCAAACCACCTAAGGTTGCATTTACAACAAGAATTTACCATCCAGATATGAACAGTAATGGCAGCATTTGTCTTGATAT
TCTAAGGTCACAGTGGTCTCCTGCCTTAACTATTTCTAAAGTTCTTTTATCCATTTGTTCACTGCTATGTGATCCGAACC
CAGATGACCAGAGATTGCACGGATCTATAAAACAGACAGAGATGAGTACAACAGAATATCTCGGGAATGGACTCAGAAGT
ATGCCATG

Alignment

ORF - retro_dord_104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.31 %
• Parental protein coverage: 58.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FKPPKVAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDD-PLVPEIAHTYKAD
          FKPPKVAFTT.IYHP..NSNGSICLDILRSQWSPALT.SKVLLSICSLLCDPNPDD.P....I..T...D
Retrocopy FKPPKVAFTTRIYHPDMNSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDD<PEIARIYKT---D

Parental  REKYNRLAREWTQKYAM
          R..YNR..REWTQKYAM
Retrocopy RDEYNRISREWTQKYAM

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_104 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.

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003997	1 retrocopy	retro_btau_1261,
Callithrix jacchus	ENSCJAG00000007875	4 retrocopies	retro_cjac_1660, retro_cjac_3666, retro_cjac_3882, retro_cjac_925,
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,
Homo sapiens	ENSG00000078967	2 retrocopies	retro_hsap_452, retro_hsap_453,
Gorilla gorilla	ENSGGOG00000003378	3 retrocopies	retro_ggor_1843, retro_ggor_2936, retro_ggor_436,
Myotis lucifugus	ENSMLUG00000011919	3 retrocopies	retro_mluc_1826, retro_mluc_1827, retro_mluc_594,
Macaca mulatta	ENSMMUG00000002410	5 retrocopies	retro_mmul_1067, retro_mmul_1937, retro_mmul_2514, retro_mmul_2515, retro_mmul_531,
Nomascus leucogenys	ENSNLEG00000003364	3 retrocopies	retro_nleu_54, retro_nleu_876, retro_nleu_90,
Oryctolagus cuniculus	ENSOCUG00000008900	1 retrocopy	retro_ocun_1058,
Pongo abelii	ENSPPYG00000029727	1 retrocopy	retro_pabe_3573,
Sus scrofa	ENSSSCG00000016722	2 retrocopies	retro_sscr_671, retro_sscr_79,
Tupaia belangeri	ENSTBEG00000003691	9 retrocopies	retro_tbel_1273, retro_tbel_2535, retro_tbel_2782, retro_tbel_307, retro_tbel_367, retro_tbel_37, retro_tbel_4118, retro_tbel_4163, retro_tbel_4312,
Tarsius syrichta	ENSTSYG00000000595	14 retrocopies	retro_tsyr_1007, retro_tsyr_1145, retro_tsyr_1162, retro_tsyr_1314, retro_tsyr_1392, retro_tsyr_1415, retro_tsyr_1677, retro_tsyr_1694, retro_tsyr_1859, retro_tsyr_683, retro_tsyr_789, retro_tsyr_836, retro_tsyr_838, retro_tsyr_919,