RetrogeneDB ID: retro_mmul_671

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214211218:864..1364(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2384
• Ensembl ID: ENSMMUG00000010207
• Aliases: None
• Description: EMG1 nucleolar protein homolog [Source:RefSeq peptide;Acc:NP_001253290]

Sequence

>retro_mmul_671
GTGGCCACGTTCAGTGTTGGAGTCCAAGCTTGCGACCAGAGTGATGGGGAGCAGGAACAGGACTGGGATGCTATGGCACC
CAAGAGGCCCTGACCTGGGGCAGGAAACCAGTTTGGAGGCCATAGCCTCCTTGTGGTGCTGGAGGAGGCCAGTCTGGAGA
CAGTCCCGGTAGGGAAGACATAAGAGCTGCTCAGCTGTGATAAGCACAAGTCTATGTTGTTGAAGAATGGACGTGACCCG
GGGGATGTGCGCTCAGACACAGCCCACCAGAATTCCCTGACGCTGCTGGATAGTCCTCTGAGATGAGCTGGCGTACTGCA
GGTCCCTGTCCACTTGCAGGAGAAGGTTCTGATTGAAGTGAGCTCCCAGACCTGAATTCCCAGAACCTTTGACCACTTTT
GTGGCCTCATGGTTCAGCTTTTACACAAGCTCAGTGTTGGAGCAGCTGATGGCCCCCAGAAGCTCTTGAAGGTAATTAAG
AATCAGTGTCAGATCACTTT

Alignment

ORF - retro_mmul_671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 68.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPSGGFKPRERSGGEQAQDWDAVPPKRPRLGAGNKIGGRRLIVVLEGASLETVKVGKTYELLNCDKHK
          .A..S.G......S.GEQ.QDWDA..PKRP..GAGN..GG..L.VVLE.ASLETV.VGKT.ELL.CDKHK
Retrocopy VATFSVGVQACDQSDGEQEQDWDAMAPKRP*PGAGNQFGGHSLLVVLEEASLETVPVGKT*ELLSCDKHK

Parental  SILLKNGRDPGEVRPDIAHQSLLMLMDSPLNRAGLLQVYIHTQKNVLIEVNPQTRIPRTFDRFCGLMVQL
          S.LLKNGRDPG.VR.D.AHQ..L.L.DSPL..AG.LQV..H.Q..VLIEV..QT.IPRTFD.FCGLMVQL
Retrocopy SMLLKNGRDPGDVRSDTAHQNSLTLLDSPLR*AGVLQVPVHLQEKVLIEVSSQT*IPRTFDHFCGLMVQL

Parental  LHKLSVRAADGPQKLLKVIKN-PVSDHF
          LHKLSV.AADGPQKLLKVIKN..VSDHF
Retrocopy LHKLSVGAADGPQKLLKVIKN<SVSDHF

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	9.97 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	13.64 RPM
SRP007412_cerebellum	0.00 RPM	10.72 RPM
SRP007412_heart	0.00 RPM	12.13 RPM
SRP007412_kidney	0.00 RPM	17.37 RPM
SRP007412_liver	0.04 RPM	9.10 RPM
SRP007412_testis	0.00 RPM	15.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_671 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_671 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013753	1 retrocopy	retro_amel_1924,
Callithrix jacchus	ENSCJAG00000007120	1 retrocopy	retro_cjac_2960,
Gorilla gorilla	ENSGGOG00000004287	1 retrocopy	retro_ggor_3077,
Macropus eugenii	ENSMEUG00000000831	1 retrocopy	retro_meug_1299,
Myotis lucifugus	ENSMLUG00000009196	1 retrocopy	retro_mluc_737,
Macaca mulatta	ENSMMUG00000010207	1 retrocopy	retro_mmul_671 ,
Nomascus leucogenys	ENSNLEG00000005080	1 retrocopy	retro_nleu_501,
Otolemur garnettii	ENSOGAG00000006975	2 retrocopies	retro_ogar_2971, retro_ogar_945,
Pongo abelii	ENSPPYG00000004215	1 retrocopy	retro_pabe_2924,
Rattus norvegicus	ENSRNOG00000012828	1 retrocopy	retro_rnor_1459,