RetrogeneDB ID: retro_mmul_2536

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:126670894..126671703(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RUVBL2
• Ensembl ID: ENSMMUG00000003915
• Aliases: None
• Description: ruvB-like 2 [Source:RefSeq peptide;Acc:NP_001253889]

Sequence

>retro_mmul_2536
GATGTGAGGAGGATTGAGCATAGAGGTGTTCACTCCCGCATCTGAGGACTGGGGCTGGATGATGCTTTGGAGGCTCAACA
GGCTTCCCAGGGCAAGGTGGGTCAGCTTTGCTGCACAGCGAGCAGCTGGTGTGGGGCTGGAGATGATCCATAAGGTGAAG
ATTGTCAAGTGGGCAGTCCTCATTGCTGGTCAGCTGGGCACAGGGAAGACAGCTATCACCCTAGGCATGGCCTAGGCCCT
GGGACCTGACACCTTGTTCATAGCCATCACTGGCAGTGAGATCTCCCTGGAGATGAGCAAGACCAAGGCACTGACACAGG
CTTTCGGGCCATCTTTTGGCATTTGCTTCAAGGAAGAGATGTAGATCATCCAAAGAGAAGTGGTTGAGACCCAGATTGAT
AGACCAGTGACAGGAATGGGCTCCAAGGTGGGCAAACTGACCATCAAAACCAAAAAGATGGAGACCATCTATGCCCTGGG
CAAGAAGATGATTGAGTCCCTGACCAAAGACAAGATCCATGCTGGTGACATGATCACTATTGACAAAGCAATGGGCAAGA
TCTCCAAATTGGGCCACTCCTTCACATGCTCCGATAACTACAGCCCCATGGACTACCAGACCAAATTCAGGCAGCCCCCA
GATGGAAAGCCCCAAAAATGCAAGGTGTACACCATATCCCTTGCACAAGATCGACATCATCAACCCCCACACCCATGGCT
TCCTGGCTCTCTTCTCATGTGACACAAGAGAGATCAAGTCAGAAGTTGCCAAGCAGATCAATGTCAAGGTGTGCGAGTGG
ATAGAACAA

Alignment

ORF - retro_mmul_2536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.44 %
• Parental protein coverage: 58.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQL-AARRAAGVVLEMIREGKIAGRAVLIAGQPGTGK
          DV.RIE..G.HS.I.GLGLDDALE..QASQG.VGQL.AA.RAAGV.LEMI...KI...AVLIAGQ.GTGK
Retrocopy DVRRIEHRGVHSRI*GLGLDDALEAQQASQGKVGQL>AAQRAAGVGLEMIHKVKIVKWAVLIAGQLGTGK

Parental  TAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQIDRPATG
          TAI..GMA.ALGPDT.F.AI.GSEI.SLEMSKT.ALTQAF..S.G...KEE..II..EVVE.QIDRP.TG
Retrocopy TAITLGMA*ALGPDTLFIAITGSEI-SLEMSKTKALTQAFGPSFGICFKEEM*IIQREVVETQIDRPVTG

Parental  TGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTK
          .GSKVGKLT.KT..METIY.LG.KMIESLTKDK..AGD.ITIDKA.GKISKLG.SFT....Y..M..QTK
Retrocopy MGSKVGKLTIKTKKMETIYALGKKMIESLTKDKIHAGDMITIDKAMGKISKLGHSFTCSDNYSPMDYQTK

Parental  FVQCPDGELQKRKEVVHTVS-LHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREE
          F.Q.PDG..QK.K..V.T.S.LH.ID.IN..T.GFLALFS.DT.EIKSEV..QIN.KV.EW.E.
Retrocopy FRQPPDGKPQKCK--VYTIS>LHKIDIINPHTHGFLALFSCDTREIKSEVAKQINVKVCEWIEQ

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	15.01 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	27.29 RPM
SRP007412_cerebellum	0.06 RPM	12.33 RPM
SRP007412_heart	0.00 RPM	16.19 RPM
SRP007412_kidney	0.00 RPM	18.66 RPM
SRP007412_liver	0.00 RPM	28.70 RPM
SRP007412_testis	0.00 RPM	153.19 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2536 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2536 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4755
Pan troglodytes	retro_ptro_3168
Gorilla gorilla	retro_ggor_2961
Pongo abelii	retro_pabe_3701

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000222	2 retrocopies	retro_cjac_329, retro_cjac_4119,
Homo sapiens	ENSG00000183207	1 retrocopy	retro_hsap_4755,
Gorilla gorilla	ENSGGOG00000009245	1 retrocopy	retro_ggor_2961,
Macropus eugenii	ENSMEUG00000000069	1 retrocopy	retro_meug_2099,
Macaca mulatta	ENSMMUG00000003915	1 retrocopy	retro_mmul_2536 ,
Nomascus leucogenys	ENSNLEG00000004769	1 retrocopy	retro_nleu_1251,
Otolemur garnettii	ENSOGAG00000007519	2 retrocopies	retro_ogar_2473, retro_ogar_3246,
Pongo abelii	ENSPPYG00000010225	1 retrocopy	retro_pabe_3701,
Pan troglodytes	ENSPTRG00000011270	1 retrocopy	retro_ptro_3168,