RetrogeneDB ID: retro_mmul_1506

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:39672913..39673521(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.17930
• Ensembl ID: ENSMMUG00000005494
• Aliases: None
• Description: ribosomal protein L10 [Source:RefSeq peptide;Acc:NP_001180488]

Sequence

>retro_mmul_1506
ATGGGCCGCCGCCCCACTGGTGTTACCATTATTGTAAGAACAACCCAAAGCCTCTCTTCTCGCGAGGTATTCCTGATGCC
AAGATTCTCATCTTTGACCTGGGGCAGAAGAGGGCAAAAGTGGTTGAGTTTCCACTCTGTGGCCACATGGTATCAGATGA
ATGGAGCCCTGGAGGCTGCCCGAATTTGTGCCAATAAGTACATGATAAAAAGTTGTGGCAAAGATGGCTTTCACATCTGA
GTGCGGCTCCACCCCTTCCACGTTATGCACATCAACAAGACGTTGTCCTGTGCTGGGCTGACAGGCTCCAAACAGGTATA
TGAGGTACCTCTGAAAAGCCCCAGGGCACTGTGGCCAGGGTTCACACTGGTCAAGTCATCGTGTCAATCAGCACCAAGCT
GCAGAACAAGGAGTATGCGATTGAGGCCCTGCACAGGGCCAAGGCCGAGCTCCCTGGCCACCAGAGGATCCACATCTCAA
AGAAGTGGGGCATTACCAAGTTCAATGTGAATGAATGCGAAGACGTGGTGGCTGAGAAACAGCTCATTCCAGATGACTGC
GGGGTCAAGTACATCCCCAATCGTGGCCCTCTGGACAAGTGGTGGGCC

Alignment

ORF - retro_mmul_1506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.56 %
• Parental protein coverage: 98.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGRRPAR-CYRYCKNKPYPKSRFCRGVPDAKIRIFDL-GRKKAKVDEFPLCGHMVSDEYEQLSSEALEAA
          MGRRP...CY.YCKN.P.P...F.RG.PDAKI.IFDL.GR...K...F....H.V...Y......ALEAA
Retrocopy MGRRPTG<CYHYCKNNPKPL--FSRGIPDAKILIFDL>GRRGQKWLSF----HSVATWYQM--NGALEAA

Parental  RICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAG-ADRLQTGMRGAFGKPQGTVARVHIGQVIMS
          RICANKYM.KSCGKDGFHI.VRLHPFHV..INK.LSCAG.ADRLQTG..G...KPQGTVARVH.GQVI.S
Retrocopy RICANKYMIKSCGKDGFHI*VRLHPFHVMHINKTLSCAG<ADRLQTGI*GTSEKPQGTVARVHTGQVIVS

Parental  IRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLD
          I.TKLQNKE..IEAL.RAK...PG.Q.IHISKKWG.TKFN..E.ED.VAEK.LIPD.CGVKYIPNRGPLD
Retrocopy ISTKLQNKEYAIEALHRAKAELPGHQRIHISKKWGITKFNVNECEDVVAEKQLIPDDCGVKYIPNRGPLD

Parental  KWRA
          KW.A
Retrocopy KWWA

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	48.74 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	215.70 RPM
SRP007412_cerebellum	0.00 RPM	55.41 RPM
SRP007412_heart	0.77 RPM	143.92 RPM
SRP007412_kidney	0.12 RPM	82.16 RPM
SRP007412_liver	0.00 RPM	287.62 RPM
SRP007412_testis	0.00 RPM	14.93 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1506 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1506 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1506 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000004369	2 retrocopies	retro_dord_14, retro_dord_715,
Echinops telfairi	ENSETEG00000001712	10 retrocopies	retro_etel_1073, retro_etel_1284, retro_etel_1517, retro_etel_1654, retro_etel_249, retro_etel_338, retro_etel_403, retro_etel_47, retro_etel_538, retro_etel_631,
Gorilla gorilla	ENSGGOG00000000131	4 retrocopies	retro_ggor_1873, retro_ggor_2425, retro_ggor_253, retro_ggor_61,
Loxodonta africana	ENSLAFG00000031860	1 retrocopy	retro_lafr_616,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Macaca mulatta	ENSMMUG00000005494	5 retrocopies	retro_mmul_1506 , retro_mmul_1654, retro_mmul_307, retro_mmul_335, retro_mmul_906,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Tupaia belangeri	ENSTBEG00000003734	1 retrocopy	retro_tbel_61,
Tarsius syrichta	ENSTSYG00000004067	7 retrocopies	retro_tsyr_11, retro_tsyr_1644, retro_tsyr_1739, retro_tsyr_1986, retro_tsyr_559, retro_tsyr_640, retro_tsyr_960,
Tursiops truncatus	ENSTTRG00000011407	7 retrocopies	retro_ttru_1085, retro_ttru_122, retro_ttru_1226, retro_ttru_1437, retro_ttru_820, retro_ttru_858, retro_ttru_867,