RetrogeneDB ID: retro_mmul_846

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:18729002..18729534(-)
• Located in intron of: ENSMMUG00000022174

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4402
• Ensembl ID: ENSMMUG00000016787
• Aliases: None
• Description: NEDD4 family-interacting protein 1 [Source:RefSeq peptide;Acc:NP_001180946]

Sequence

>retro_mmul_846
ATGGAGTTGGCATTAGTGGCACCAGTGGCAGTTGAGCTGGTCTGCAGCAGCAGGTACCAACATTTATAGAATGAAGAAGA
GCCTGAGGAACCTGAGAAGGCTTCAGGTGAGGTTCCTCCATCTTATGGCATCAACTCTGCAGAGAGTATGGTGTATTTGA
CTACAATGATGAGTCTAATTTTCCAAAGCCCCTGTTTTACAATGTGGTTGTAAACATTACCAATTTATAATCAAGTCATG
AGAATTAAGGCTGAAGCTATTTCTTTGGTTCCTGGAAGAGATGAGGATTTTGTGGGACGGGATGATTTTGATGATGCTGA
CCAGCTGAGGATACGAATTTTTTTTTTTTTTTTGGTTAACTTTTTCCTGGCATTCTTCTTAACTGGATTAAGTTTTTTCC
TGTCTTTTTGCCTGACTGCTTCAGTGGCAGGAAGGTATGACACCCATGTCAGAATTTGGTCTCTTTCTAATTAAGTGGGT
CCTGAGAGTCAGATTTCTAACCTGTTTTCCTTGATACGTTCATGGTCAGCAC

Alignment

ORF - retro_mmul_846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.88 %
• Parental protein coverage: 80.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALALAALAAVEPACGSRYQQLQNEEESGEPEQAAGDAPPPYSSISAESAAY-FDYKDESGFPKPPSYNV
          M.LAL.A..AVE..C.SRYQ.L.NEEE..EPE.A.G..PP.Y...SAES..Y.FDY.DES.FPKP..YNV
Retrocopy MELALVAPVAVELVCSSRYQHL*NEEEPEEPEKASGEVPPSYGINSAESMVY<FDYNDESNFPKPLFYNV

Parental  AT-TLPSYDEAERTKAEATIPLVPGRDEDFVGRDDFDDADQLRIGNDGIFMLTFFMAFLFNWIGFFLSFC
          ...TLP.Y....R.KAEA.I.LVPGRDEDFVGRDDFDDADQLRI.........FF.AF......FFLSFC
Retrocopy VV>TLPIYNQVMRIKAEA-ISLVPGRDEDFVGRDDFDDADQLRIRXXXXXXVNFFLAFFLTGLSFFLSFC

Parental  LTTSAAGRYGA-ISGFGLSLIKWILIVRFSTYFPGYFDGQY
          LT.S.AGRY....S.FGL.LIKW.L.VRF.T.FP.Y..GQ.
Retrocopy LTASVAGRYDT>MSEFGLFLIKWVLRVRFLTCFP*YVHGQH

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	251.33 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	196.58 RPM
SRP007412_cerebellum	0.00 RPM	187.01 RPM
SRP007412_heart	0.00 RPM	54.88 RPM
SRP007412_kidney	0.00 RPM	125.12 RPM
SRP007412_liver	0.04 RPM	49.52 RPM
SRP007412_testis	0.00 RPM	40.14 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_846 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_846 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_846 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1091
Pan troglodytes	retro_ptro_743
Gorilla gorilla	retro_ggor_859
Pongo abelii	retro_pabe_908
Callithrix jacchus	retro_cjac_3175

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047747	1 retrocopy	retro_btau_766,
Callithrix jacchus	ENSCJAG00000018271	1 retrocopy	retro_cjac_3175,
Equus caballus	ENSECAG00000021907	1 retrocopy	retro_ecab_261,
Homo sapiens	ENSG00000131507	1 retrocopy	retro_hsap_1091,
Gorilla gorilla	ENSGGOG00000004879	1 retrocopy	retro_ggor_859,
Macaca mulatta	ENSMMUG00000016787	1 retrocopy	retro_mmul_846 ,
Pongo abelii	ENSPPYG00000015896	1 retrocopy	retro_pabe_908,
Pan troglodytes	ENSPTRG00000017358	1 retrocopy	retro_ptro_743,
Sarcophilus harrisii	ENSSHAG00000002466	1 retrocopy	retro_shar_738,
Sus scrofa	ENSSSCG00000025295	1 retrocopy	retro_sscr_301,
Ictidomys tridecemlineatus	ENSSTOG00000005153	1 retrocopy	retro_itri_1454,