RetrogeneDB ID: retro_mmul_1761

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:38933322..38933802(+)
• Located in intron of: ENSMMUG00000015747

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000008983
• Aliases: None
• Description: None

Sequence

>retro_mmul_1761
AATGGCCATGTGGAAGCAGTCACTCTCCAGGTGAACTGAAAATGCCAGACTGACATTGGTGGCAAACGAAACAGGATGCC
TTTGATGAAGGCTGTACATTGCCAGGAAGAGATTTGTGTCATCACTCTGCTAGAACGTGGCACCAATCCAGATCTTATGG
ATGTCTACAGCAACAACGCACTACACTATGCTATCTATAATGAGAACACACTACTGGCAGAAAAACTGCCTTCACACCAT
GTGAATACTGAAGTGCTGAACAAGCATGGAAACACACCACTTTATAGTTTGCAAAACACAGCAAAAGGTGGAATTTTAGT
GAAGAAACAAGCAAATGTACATGCTGTTGATAGGTTGAAAAGAACAGCCCTCATGGCTGTTGTACATTATGGCTTGTCAG
GTATAGTTAGCATTCTTCTTCAACAAAGTATATGCATACTCAAGAGTATGTATTAACAGACTGCAGAAGATCATGCTATT

Alignment

ORF - retro_mmul_1761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.1 %
• Parental protein coverage: 62.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HGHIEVVTLLLRRRCQIDIYDRLNRTPLMKAVHCQEEACAIILLERGANPNIKDIYGNTALHYAVYNKGT
          .GH.E.VTL.....CQ.DI....NR.PLMKAVHCQEE.C.I.LLERG.NP...D.Y.N.ALHYA.YN..T
Retrocopy NGHVEAVTLQVN*KCQTDIGGKRNRMPLMKAVHCQEEICVITLLERGTNPDLMDVYSNNALHYAIYNENT

Parental  SLAEKLLSHHANIEALNEEGNTPLLFAINSRRQQMVEFLLKNQANIHAVDNYRRTALMLAVQHNSSSIVS
          .LAEKL.SHH.N.E.LN..GNTPL....N.........L.K.QAN.HAVD...RTALM..V....S.IVS
Retrocopy LLAEKLPSHHVNTEVLNKHGNTPLYSLQNTAKGGI---LVKKQANVHAVDRLKRTALMAVVHYGLSGIVS

Parental  LLLQQNVNIFSQDMFGQTAEDYAV
          .LLQQ...I....M..QTAED.A.
Retrocopy ILLQQSICIL-KSMY*QTAEDHAI

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	1.23 RPM	0.11 RPM
SRP007412_brain_prefrontal_cortex	1.35 RPM	0.08 RPM
SRP007412_cerebellum	0.52 RPM	0.06 RPM
SRP007412_heart	0.71 RPM	0.12 RPM
SRP007412_kidney	2.11 RPM	0.00 RPM
SRP007412_liver	1.07 RPM	0.08 RPM
SRP007412_testis	3.77 RPM	4.71 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1761 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1761 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_2331

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008211	2 retrocopies	retro_cjac_2331, retro_cjac_2672,
Microcebus murinus	ENSMICG00000017899	2 retrocopies	retro_mmur_1151, retro_mmur_246,
Macaca mulatta	ENSMMUG00000008983	1 retrocopy	retro_mmul_1761 ,
Nomascus leucogenys	ENSNLEG00000016858	1 retrocopy	retro_nleu_2713,
Pongo abelii	ENSPPYG00000019046	1 retrocopy	retro_pabe_1037,
Tupaia belangeri	ENSTBEG00000017150	1 retrocopy	retro_tbel_490,