RetrogeneDB ID: retro_mmul_268

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:26505914..26506361(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030448
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.2933
• Ensembl ID: ENSMMUG00000021828
• Aliases: None
• Description: ribosomal protein L27a [Source:RefSeq peptide;Acc:NP_001180496]

Sequence

>retro_mmul_268
ATGCCATCCAGACTGAGGAAGACCCGGAAACTTTGGGGCCACGTGAGCCACGGCCACGGCCGCATAGGCAAGCACCGGAA
GCACCCCGGAGGCCGCGGTAATGCTGGTGGTCTGCATCACCACCGGATCAACTTCGACAAATACCACCCAGGCTACTTTG
GGAAAGTTGGTATGAGGCATTACCACTTAAAGAGGAACCAGAGCTTCTGCCCAACTGTCAACCTTGACAAATTGTGGACT
TTGGTCAGTGAGCAGACACGGGTGAATGCTGCTAAAAACAAGACTGGGGCTGCTCCCATCATTGATGTGGTGCGATTGGG
CTACTACAAAGTTCTGGGAAAGGGAAAGCTCCCAAAGCAGCCTGTCATTGTGAAGGCCAAATTCTTCAGCAGAAGAGCTG
AGGAGAAGATTAAGGGTGTTGGGGGGGCCTGTGTCCTGGTGGCTTGA

Alignment

ORF - retro_mmul_268 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGLHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFC
          MPSRLRKTRKL.GHVSHGHGRIGKHRKHPGGRGNAGGLHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFC
Retrocopy MPSRLRKTRKLWGHVSHGHGRIGKHRKHPGGRGNAGGLHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFC

Parental  PTVNLDKLWTLVSEQTRVNAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGV
          PTVNLDKLWTLVSEQTRVNAAKNKTGAAPIIDVVR.GYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGV
Retrocopy PTVNLDKLWTLVSEQTRVNAAKNKTGAAPIIDVVRLGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGV

Parental  GGACVLVA
          GGACVLVA
Retrocopy GGACVLVA

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	0.11 RPM	65.33 RPM
SRP007412_brain_prefrontal_cortex	0.71 RPM	168.26 RPM
SRP007412_cerebellum	0.00 RPM	73.87 RPM
SRP007412_heart	0.29 RPM	126.49 RPM
SRP007412_kidney	0.35 RPM	130.16 RPM
SRP007412_liver	0.36 RPM	198.28 RPM
SRP007412_testis	0.23 RPM	59.03 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_268 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_268 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_268 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ficedula albicollis	ENSFALG00000000924	1 retrocopy	retro_falb_20,
Homo sapiens	ENSG00000166441	7 retrocopies	retro_hsap_1263, retro_hsap_1908, retro_hsap_2352, retro_hsap_239, retro_hsap_3335, retro_hsap_3586, retro_hsap_3682,
Gorilla gorilla	ENSGGOG00000001660	2 retrocopies	retro_ggor_155, retro_ggor_1785,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Macaca mulatta	ENSMMUG00000021828	2 retrocopies	retro_mmul_207, retro_mmul_268 ,
Monodelphis domestica	ENSMODG00000007480	1 retrocopy	retro_mdom_575,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40,
Nomascus leucogenys	ENSNLEG00000017535	1 retrocopy	retro_nleu_102,
Pan troglodytes	ENSPTRG00000003333	1 retrocopy	retro_ptro_33,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Tupaia belangeri	ENSTBEG00000000046	20 retrocopies	retro_tbel_1093, retro_tbel_1101, retro_tbel_1148, retro_tbel_1152, retro_tbel_1223, retro_tbel_1338, retro_tbel_1639, retro_tbel_2017, retro_tbel_2606, retro_tbel_2777, retro_tbel_298, retro_tbel_3111, retro_tbel_3496, retro_tbel_3881, retro_tbel_4566, retro_tbel_460, retro_tbel_544, retro_tbel_643, retro_tbel_925, retro_tbel_937,
Taeniopygia guttata	ENSTGUG00000008355	1 retrocopy	retro_tgut_18,
Tarsius syrichta	ENSTSYG00000013207	16 retrocopies	retro_tsyr_1103, retro_tsyr_155, retro_tsyr_1591, retro_tsyr_1607, retro_tsyr_1623, retro_tsyr_170, retro_tsyr_1725, retro_tsyr_187, retro_tsyr_204, retro_tsyr_283, retro_tsyr_498, retro_tsyr_50, retro_tsyr_550, retro_tsyr_608, retro_tsyr_612, retro_tsyr_716,