RetrogeneDB ID: retro_mmul_3

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:30131913..30132261(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000031038
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LSM12
• Ensembl ID: ENSMMUG00000006804
• Aliases: None
• Description: protein LSM12 homolog [Source:RefSeq peptide;Acc:NP_001253722]

Sequence

>retro_mmul_3
GGCTCCTCCCGGCGAGTATATAGCGTTGGGAGCCAGGTGTCGAGCGGGGCGTGCCAGGAGCAGCGGCTGCAGGGCGAGGT
GGTAGCCTTTGACCACCAATCCAAAATGCTGGCTTTAAAATGTCCCTCTTCCAATGGAAAGCCCAACCATGCAGACATCT
TGCTCATAAACTTACAGTATGTTTCCGAAGTGGAAATAATTAATGACCGAACAGAAACCCCTCCTCCCCTAGCTGCACTC
AATGTTAGTAAGCTTGCCAGCAAAGCACGGACAGAGAAGGAGGAAAAGCTGAGTCAGGCCTATGCAATCAGTGCTGGTGT
CTCTCTAGAGGGCCAGCAGCTCTTCTAG

Alignment

ORF - retro_mmul_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.58 %
• Parental protein coverage: 55.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIINDRTETPPP
          .SVGSQVS...CQEQRLQGEVVAFD.QSKMLALKCPSS.GKPNHADILLINLQYVSEVEIINDRTETPPP
Retrocopy YSVGSQVSSGACQEQRLQGEVVAFDHQSKMLALKCPSSNGKPNHADILLINLQYVSEVEIINDRTETPPP

Parental  LASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLF
          LA.LNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLF
Retrocopy LAALNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLF

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	29.47 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	33.79 RPM
SRP007412_cerebellum	0.00 RPM	23.83 RPM
SRP007412_heart	0.00 RPM	20.08 RPM
SRP007412_kidney	0.00 RPM	26.99 RPM
SRP007412_liver	0.00 RPM	14.41 RPM
SRP007412_testis	0.38 RPM	64.98 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_3 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_3 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_3 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014379	2 retrocopies	retro_cfam_1843, retro_cfam_312,
Choloepus hoffmanni	ENSCHOG00000001198	1 retrocopy	retro_chof_1429,
Dipodomys ordii	ENSDORG00000016381	1 retrocopy	retro_dord_596,
Erinaceus europaeus	ENSEEUG00000002419	1 retrocopy	retro_eeur_603,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Felis catus	ENSFCAG00000029083	1 retrocopy	retro_fcat_787,
Homo sapiens	ENSG00000161654	1 retrocopy	retro_hsap_4041,
Loxodonta africana	ENSLAFG00000005202	1 retrocopy	retro_lafr_906,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Myotis lucifugus	ENSMLUG00000006391	1 retrocopy	retro_mluc_2205,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3 ,
Mus musculus	ENSMUSG00000020922	1 retrocopy	retro_mmus_2683,
Otolemur garnettii	ENSOGAG00000010489	2 retrocopies	retro_ogar_1771, retro_ogar_2447,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Pteropus vampyrus	ENSPVAG00000013706	1 retrocopy	retro_pvam_172,
Rattus norvegicus	ENSRNOG00000020894	1 retrocopy	retro_rnor_2845,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,
Vicugna pacos	ENSVPAG00000011145	1 retrocopy	retro_vpac_627,