RetrogeneDB ID: retro_mmul_1060

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:53261366..53262013(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2791
• Ensembl ID: ENSMMUG00000021976
• Aliases: None
• Description: None

Sequence

>retro_mmul_1060
ATGGATGGCAAGACAGGGCTGTTCCGAGGTCTGAGCCTCCGACTGATGTGACCCCTCTCCTTTGTAACGGGGGCAGCAGG
AAGGTTTTCCCTCCAGATGAAATCAAGCAGGTTTCCAATAAGGATGGATATGAAGACTTCTCTGAAGCAGGCAGTGAAGG
AGACCTCCTAGGGGATGATGATGCAGTGTGTGTCCTGTATGTTGGCCCACCCCCTGCATGCCATCTCAATGTGCTGCATG
GTCTAATTTGTGGGATGGGAGGTCAAGTACAGTGGTGTCCTGAGCTCCACTGAGAAGATTTTCAAAGAGGAAGGGCTGCT
GGGATTCTTTGTTGGCTTGATCTTTCATCTCCTGGGTGAAGTAGTTTTCTTGTGAAGCTATAACCTGCTGGCCCACTTTT
ATCAATGACTACCTGGTAGATGACAGCGTGATTGACACCTAGGGGGGCTGAGAAATGACCAGAATTGGGGTTCCCAGTTA
GGCCAGGCCCTGTCCATCCAGAGCTACATCAAGTTTGTGATGGAGATTGCAGTGAGCATGCTGACCTCCCCTTTCCTGCT
GGTCGGCAGCCTCATGGCTGTGAACAACTGTGGGCCCAGGCTGGGCTCTCGCCTTACTCGCTGGTGTTCAAATCCTGGAT
TAACTGC

Alignment

ORF - retro_mmul_1060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.58 %
• Parental protein coverage: 56.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VDGKIGLFRGLSPRLMSNALSTVT-RGSMKKVFPPDEIEQVSNKD-DMKTSLKKVVKETSYEMMMQCVSR
          .DGK.GLFRGLS.RLM...LS.VT..GS.K.VFPPDEI.QVSNKD.DMKTSLK..VKETS..MMMQCVS.
Retrocopy MDGKTGLFRGLSLRLM-*PLSFVT<GGSRK-VFPPDEIKQVSNKD>DMKTSLKQAVKETS*GMMMQCVSC

Parental  MLAHPLHVISMRCMVQFVGREAKYSGVLSSIGKIFKEEGLLGFFVGLIPHLLGDVVFLWGCNLLAH-FIN
          MLAHPLH.ISM.CMV.FVG.E.KYSGVLSS..KIFKEEGLLGFFVGLI.HLLG.VVFL...NLLAH.FIN
Retrocopy MLAHPLHAISMCCMV*FVGWEVKYSGVLSSTEKIFKEEGLLGFFVGLIFHLLGEVVFL*SYNLLAH>FIN

Parental  AYLVDDSVSDT-PGGLGNDQNPGSQFSQALAIRSYTKFVMGIAVSMLTYPFLLVGDLMAVNNCG-LQAGL
          .YLVDDSV.DT..GGL.NDQN.GSQ..QAL.I.SY.KFVM.IAVSMLT.PFLLVG.LMAVNNCG..QAGL
Retrocopy DYLVDDSVIDT<LGGLRNDQNWGSQLGQALSIQSYIKFVMEIAVSMLTSPFLLVGSLMAVNNCG<AQAGL

Parental  PPYSPVFKSWIHC
          .PYS.VFKSWI.C
Retrocopy SPYSLVFKSWINC

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	0.22 RPM	256.60 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	538.97 RPM
SRP007412_cerebellum	0.19 RPM	142.13 RPM
SRP007412_heart	0.00 RPM	87.15 RPM
SRP007412_kidney	0.12 RPM	115.61 RPM
SRP007412_liver	0.00 RPM	84.12 RPM
SRP007412_testis	0.11 RPM	26.42 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1060 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1060 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1060 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_691

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000137409	2 retrocopies	retro_hsap_3671, retro_hsap_856,
Gorilla gorilla	ENSGGOG00000003908	1 retrocopy	retro_ggor_2481,
Macaca mulatta	ENSMMUG00000021976	1 retrocopy	retro_mmul_1060 ,
Nomascus leucogenys	ENSNLEG00000010899	1 retrocopy	retro_nleu_423,
Pongo abelii	ENSPPYG00000016557	2 retrocopies	retro_pabe_3011, retro_pabe_691,
Pan troglodytes	ENSPTRG00000018115	1 retrocopy	retro_ptro_2490,
Tarsius syrichta	ENSTSYG00000014777	1 retrocopy	retro_tsyr_488,
Tursiops truncatus	ENSTTRG00000001966	2 retrocopies	retro_ttru_1101, retro_ttru_563,