RetrogeneDB ID: retro_mmul_1828

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:35847400..35848050(-)
• Located in intron of: ENSMMUG00000008444

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT5
• Ensembl ID: ENSMMUG00000017141
• Aliases: None
• Description: ADP-sugar pyrophosphatase [Source:RefSeq peptide;Acc:NP_001247879]

Sequence

>retro_mmul_1828
GACAGCCAAGAACCAACTGAATCTTCTCAGAATGGAAACACTGTATTATTTTGGAGGAGTTAATTTCAGAAGGAAAATGG
GTCAAGCTTGAAAAAACAACGTAGGTGGCTCCTACTGGTAAAACTGGAACTTGGGACTCAGTGAAACGTACAACCAGGAA
AGAACAGACTGGTGATGATGCAGCGATCATCCCTGTGCTGCAGAGAACGCTTCACTACGAGTGTATCATTCTGGTGAAAC
AGTCCTGACGACCAACAGGTGGCTACTGCATAGAGTTCCCTGCAGGTCTCATAGATTATGGTGAAATCCCAGGAGCAGCT
GCTCTTCGGGAGCTTGAAGAAGAAACTGGCTACTAGGGGGACACTGCCGAAAGTTCTCCAGTGGTCTGTATGGACCCAAG
TTTGTCAAACTGTACCACACACATTGTGACAGTAATCATTAACGGAGATGATATAGAAAATCTAAGGCCCAAGCCAACGC
CAGGGGATGGAGAATTTGTGGAAGTCATTTCGTTACCCAAGAATGACCTGCTGCAGAGACTCGATGCTCTCATAGCTGAA
GAACATCTTACAGTGGATGCCAGAGTCTATTCCTATGCTCTAGTGCTGAAACATGCAAATGTGAAGCCATTTGAAGTGCC
CACCCTGAAA

Alignment

ORF - retro_mmul_1828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.03 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESQEPTQSSQNG-KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVAVIPVLQR
          .SQEPT.SSQNG.K..II.EELISEGKWVKLEKTT...PTGKT.TW.SVKRTTRKEQT.D..A.IPVLQR
Retrocopy DSQEPTESSQNG<KHCIILEELISEGKWVKLEKTT*VAPTGKTGTWDSVKRTTRKEQTGDDAAIIPVLQR

Parental  TLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETGYKGDVAECSPAVCMDPGLSNCT
          TLHYECI.LVKQ...P.GGYCIEFPAGLID.GE.P.AAALRELEEETGY.GD.AE.SP.VCMDP.LSNCT
Retrocopy TLHYECIILVKQS*RPTGGYCIEFPAGLIDYGEIPGAAALRELEEETGY*GDTAESSPVVCMDPSLSNCT

Parental  THIVTVTINGDDAENARPKPKPGDGEFVEVISLPKNDLLQRLHALVAEEHLTVDARVYSYALALKHANAK
          THIVTV.INGDD.EN.RPKP.PGDGEFVEVISLPKNDLLQRL.AL.AEEHLTVDARVYSYAL.LKHAN.K
Retrocopy THIVTVIINGDDIENLRPKPTPGDGEFVEVISLPKNDLLQRLDALIAEEHLTVDARVYSYALVLKHANVK

Parental  PFEVPFLK
          PFEVP.LK
Retrocopy PFEVPTLK

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	0.11 RPM	10.20 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.54 RPM
SRP007412_cerebellum	0.52 RPM	11.04 RPM
SRP007412_heart	0.06 RPM	5.48 RPM
SRP007412_kidney	0.23 RPM	15.96 RPM
SRP007412_liver	0.12 RPM	12.07 RPM
SRP007412_testis	0.04 RPM	3.54 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1828 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1828 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3580
Pan troglodytes	retro_ptro_2427
Gorilla gorilla	retro_ggor_2415
Pongo abelii	retro_pabe_2949

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019509	2 retrocopies	retro_btau_1326, retro_btau_1438,
Canis familiaris	ENSCAFG00000004794	2 retrocopies	retro_cfam_435, retro_cfam_612,
Equus caballus	ENSECAG00000023658	1 retrocopy	retro_ecab_647,
Echinops telfairi	ENSETEG00000006403	1 retrocopy	retro_etel_946,
Felis catus	ENSFCAG00000025093	1 retrocopy	retro_fcat_350,
Homo sapiens	ENSG00000165609	1 retrocopy	retro_hsap_3580,
Gorilla gorilla	ENSGGOG00000006325	1 retrocopy	retro_ggor_2415,
Loxodonta africana	ENSLAFG00000012052	1 retrocopy	retro_lafr_226,
Myotis lucifugus	ENSMLUG00000010453	2 retrocopies	retro_mluc_1263, retro_mluc_2073,
Macaca mulatta	ENSMMUG00000017141	1 retrocopy	retro_mmul_1828 ,
Nomascus leucogenys	ENSNLEG00000012298	1 retrocopy	retro_nleu_2838,
Oryctolagus cuniculus	ENSOCUG00000009308	1 retrocopy	retro_ocun_862,
Otolemur garnettii	ENSOGAG00000005816	2 retrocopies	retro_ogar_2071, retro_ogar_2988,
Pongo abelii	ENSPPYG00000002091	2 retrocopies	retro_pabe_2949, retro_pabe_3040,
Pan troglodytes	ENSPTRG00000002294	1 retrocopy	retro_ptro_2427,
Rattus norvegicus	ENSRNOG00000017741	1 retrocopy	retro_rnor_1672,
Sus scrofa	ENSSSCG00000011113	1 retrocopy	retro_sscr_143,
Tursiops truncatus	ENSTTRG00000007394	2 retrocopies	retro_ttru_209, retro_ttru_495,