RetrogeneDB ID: retro_mmul_2515

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:87611537..87611920(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D4
• Ensembl ID: ENSMMUG00000002410
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 4 (putative) [Source:HGNC Symbol;Acc:21647]

Sequence

>retro_mmul_2515
ATGTAACTGAAGCAGATTACTAAGGAATTTAGGATTTTTGTCCTTGGTCCTCTAGCACAGTGTTCTGTTGGATGTTATAG
GTTTCATTGGCAGGCTACAATTATAGGACCTCCTTGCCGCCTGTATCAAGGTGGGTGTGTTCTTGACACTTCATTTTCAT
TCAGACTACCCCTTCAAACCACCTAAAGTTGCATTTATTACAATAATTTATCATCCAAACATTTATAGTAATGAGAGCAT
TTGTCTCAGTATTCTAAGATCACTGTGGTCTTCTGCTTTAACATTTTTAAAGTTATTTTTACATCAATTTGTTCACTGTT
ATGTGATCCAAATCCAGAAACCCCCTAGTGCTAGAGATTGCAGAGACCTATAAAACAGACAAA

Alignment

ORF - retro_mmul_2515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.19 %
• Parental protein coverage: 89.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALKRIQKELTDLQRDPPAQCSAGPVGDDLFHWQATIMGPNDSPYQG-GVFFLTIHFPTDYPFKPPKVAF
          M.LK.I.KE.......P.AQCS...VG...FHWQATI.GP....YQG.GVF.LT.HF..DYPFKPPKVAF
Retrocopy M*LKQITKEFRIFVLGPLAQCS---VGCYRFHWQATIIGPPCRLYQG>GVF-LTLHFHSDYPFKPPKVAF

Parental  TTKIYHPNINSNGSICLDILRSQWSPALT-VSKVLL-SICSLLCDPNPD-DPLVPEIAHTYKADR
          .T.IYHPNI.SN.SICL.ILRS.WS.ALT...KV...SICSLLCDPNP...PLV.EIA.TYK.D.
Retrocopy ITIIYHPNIYSNESICLSILRSLWSSALT<IFKVIFTSICSLLCDPNPE<NPLVLEIAETYKTDK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	27.45 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	35.14 RPM
SRP007412_cerebellum	0.00 RPM	21.25 RPM
SRP007412_heart	0.00 RPM	24.91 RPM
SRP007412_kidney	0.00 RPM	28.05 RPM
SRP007412_liver	0.00 RPM	27.35 RPM
SRP007412_testis	0.00 RPM	68.79 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2515 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2515 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3670

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 58 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	ENSDORG00000006888	5 retrocopies	retro_dord_104, retro_dord_345, retro_dord_408, retro_dord_743, retro_dord_760,
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,
Macaca mulatta	ENSMMUG00000008069	2 retrocopies	retro_mmul_1382, retro_mmul_1834,
Macaca mulatta	ENSMMUG00000020666	3 retrocopies	retro_mmul_1298, retro_mmul_2143, retro_mmul_2246,
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,