RetrogeneDB ID: retro_mmul_715

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214740492:7467..8057(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11H12orf29
• Ensembl ID: ENSMMUG00000015860
• Aliases: None
• Description: None

Sequence

>retro_mmul_715
ACTCACCCTGCTTGTTGGGCTCACCAAGAGGTGCCTGGGCTCCATGCAGCAAAAAATATCATGTGTGTTTGTGATGGAAG
TGGAAGAGGAGCCTTCTGCCAAAAGGAGCAGCAGATTAGCCACACCTGTGGGCTCAACTAGATAGAAAACCTAACAAACA
AGCCGAAAAAAGATTTTACATTTTTCTACATTCAAAAGAAAACACCAAAGAATTTTTTGGGAACCTTGAGGAGGACTTCA
AACAGGCTCCAGAGTGCTGCATACCAGCAAAGGAAATAGGACAACGAAATGGGAATCCAGCACCCGATGAAAATGGACAT
ATTCTTAGTTGAGTACCAGTAGAAAAAAACAATAAACAGTACTGCTGGCATTCCTCTGTAGTTCATTATGAATTTGAAAT
TGCCCTGATACTAAAGCATCATCCTGATGAACCTGGGCTTTTGGAAATAAGTGTAGTGCCACTAATTTTAGAACAAACAC
TGGAGCTTATAGGAACAAATATCAATGGAAACCCATGTGGGTTAGGAAGCAAGACGCATCCATTACATCTTCTTATACCA
CATGGAGCATTCCAAATAAGAAATCTACCC

Alignment

ORF - retro_mmul_715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.5 %
• Parental protein coverage: 60.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TRTACWAHHEALGLGAAENAVCVCDGGERGAFRQK-GASDQPYLWARLDRKPNKQAEKRFKNFLHSKENP
          T..ACWAH.E..GL.AA.N..CVCDG..RGAF.QK.GA.D.P.LWA.LDRKPNKQAEKRF..FLHSKEN.
Retrocopy THPACWAHQEVPGLHAAKNIMCVCDGSGRGAFCQK<GAAD*PHLWAQLDRKPNKQAEKRFYIFLHSKENT

Parental  KEFFWNVEEDFKPAPECWIPAKEIEQINGNPVPDENGHIPGWVPVEKNNKQYCWHSSVVNYEFEIALVLK
          KEFF.N.EEDFK.APEC.IPAKEI.Q.NGNP.PDENGHI...VPVEKNNKQYCWHSSVV.YEFEIAL.LK
Retrocopy KEFFGNLEEDFKQAPECCIPAKEIGQRNGNPAPDENGHILS*VPVEKNNKQYCWHSSVVHYEFEIALILK

Parental  HHPDDSGLLEISAVPLSDLLEQTLELIGTNINGNPYGLGSKKHPLHLLIPHGAFQVRNLP
          HHPD..GLLEIS.VPL...LEQTLELIGTNINGNP.GLGSK.HPLHLLIPHGAFQ.RNLP
Retrocopy HHPDEPGLLEISVVPL--ILEQTLELIGTNINGNPCGLGSKTHPLHLLIPHGAFQIRNLP

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	11.54 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.66 RPM
SRP007412_cerebellum	0.00 RPM	14.46 RPM
SRP007412_heart	0.00 RPM	1.53 RPM
SRP007412_kidney	0.00 RPM	4.58 RPM
SRP007412_liver	0.00 RPM	1.66 RPM
SRP007412_testis	0.00 RPM	36.52 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_715 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_715 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011011	1 retrocopy	retro_chof_1262,
Homo sapiens	ENSG00000133641	1 retrocopy	retro_hsap_3984,
Gorilla gorilla	ENSGGOG00000005986	1 retrocopy	retro_ggor_2674,
Loxodonta africana	ENSLAFG00000013286	1 retrocopy	retro_lafr_706,
Macaca mulatta	ENSMMUG00000015860	1 retrocopy	retro_mmul_715 ,
Nomascus leucogenys	ENSNLEG00000005396	1 retrocopy	retro_nleu_1905,
Pan troglodytes	ENSPTRG00000005277	1 retrocopy	retro_ptro_2704,
Rattus norvegicus	ENSRNOG00000006973	1 retrocopy	retro_rnor_1625,
Tupaia belangeri	ENSTBEG00000005256	1 retrocopy	retro_tbel_94,
Tarsius syrichta	ENSTSYG00000014665	1 retrocopy	retro_tsyr_1572,