RetrogeneDB ID: retro_mmul_2610

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:85619034..85619577(-)
• Located in intron of: ENSMMUG00000016777

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4403
• Ensembl ID: ENSMMUG00000021605
• Aliases: None
• Description: None

Sequence

>retro_mmul_2610
GGAGGAACTGCTGTTCCCCCAGTGTATGGTCAGCTTCTAGCTTTTTATTTGCTCCATAACGACAAGAATAACTCAAGATA
TCTTTGGTAAAGAATACCACCTGCTATAAAATCTGCAAATTCTGAACTTGGGAGAATTTGCTCAGTAGGAAAAAAATTCT
GGCATAGAGATTTCCTTGGGATGTATACAACCCTCAATGCTTACCAGTAGCCTAAGATGTTCCAGTCAATTATGGAAGCA
CTTAGAGATACAACAAGGAGATGAGCCTTTGCCTTGCCCTTTCAAGCATATATCTCAATAACGGCTGATGATTTTGCAGC
CTTTGTTGGACGTCCTGTAGAAGAGTCTGTGAAAAGTACATTAAAACAAGAATGGCAAGCTGACCCCACCATAAGAATGG
TTATGCCCAGAAAGCCAACTGCAAGGGCCCCAGATGTTTCTTTTAACAAGTTTATTCTCTTGCCAGAGTGAATTCCAGTT
CACCCAATCTCCAGTGAATAGCAGTTATCCAGATGGACGGGTTATGTGGTTTTCCTTGATAAC

Alignment

ORF - retro_mmul_2610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.72 %
• Parental protein coverage: 98.91 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGIATPPVYGQLLALYLLHNDMNNARYLWKRIPPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQW
          GG.A.PPVYGQLLA.YLLHND.NN.RYLW.RIPPAIKSANSELG.I.SVG...W.RDF.G.YTT.NA.Q.
Retrocopy GGTAVPPVYGQLLAFYLLHNDKNNSRYLW*RIPPAIKSANSELGRICSVGKKFWHRDFLGMYTTLNAYQ*

Parental  SETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPV
          ....Q.IMEALRD.TRR.AFAL..QAY.SI.ADDFAAFVG.PVEE.VK..L.Q.WQAD.T.RMV.PRKP.
Retrocopy PKMFQSIMEALRDTTRR*AFALPFQAYISITADDFAAFVGRPVEESVKSTLKQEWQADPTIRMVMPRKPT

Parental  AGALDVSFNKFIPLSEPAPVPPIPNEQQLARLTDYVAFLEN
          A.A.DVSFNKFI.L.E..PV.PI..E.QL.R.T.YV.FL.N
Retrocopy ARAPDVSFNKFILLPE*IPVHPISSE*QLSRWTGYVVFLDN

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	84.37 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	61.72 RPM
SRP007412_cerebellum	0.00 RPM	69.09 RPM
SRP007412_heart	0.00 RPM	32.74 RPM
SRP007412_kidney	0.00 RPM	42.02 RPM
SRP007412_liver	0.00 RPM	12.23 RPM
SRP007412_testis	0.00 RPM	83.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2610 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2610 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2610 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4869
Pongo abelii	retro_pabe_3787
Callithrix jacchus	retro_cjac_4193

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005854	3 retrocopies	retro_btau_1315, retro_btau_1401, retro_btau_1402,
Canis familiaris	ENSCAFG00000030168	1 retrocopy	retro_cfam_1327,
Callithrix jacchus	ENSCJAG00000002267	1 retrocopy	retro_cjac_4193,
Dasypus novemcinctus	ENSDNOG00000015309	5 retrocopies	retro_dnov_1157, retro_dnov_1306, retro_dnov_149, retro_dnov_1701, retro_dnov_527,
Homo sapiens	ENSG00000198612	2 retrocopies	retro_hsap_2657, retro_hsap_4869,
Macropus eugenii	ENSMEUG00000008189	3 retrocopies	retro_meug_583, retro_meug_609, retro_meug_701,
Macaca mulatta	ENSMMUG00000021605	1 retrocopy	retro_mmul_2610 ,
Monodelphis domestica	ENSMODG00000007474	1 retrocopy	retro_mdom_1295,
Mustela putorius furo	ENSMPUG00000000068	1 retrocopy	retro_mputfur_176,
Mus musculus	ENSMUSG00000034432	1 retrocopy	retro_mmus_1812,
Nomascus leucogenys	ENSNLEG00000010706	2 retrocopies	retro_nleu_1528, retro_nleu_2002,
Oryctolagus cuniculus	ENSOCUG00000007341	4 retrocopies	retro_ocun_1549, retro_ocun_1579, retro_ocun_428, retro_ocun_550,
Pongo abelii	ENSPPYG00000013308	1 retrocopy	retro_pabe_3787,
Rattus norvegicus	ENSRNOG00000019635	3 retrocopies	retro_rnor_1005, retro_rnor_1078, retro_rnor_975,
Ictidomys tridecemlineatus	ENSSTOG00000022662	4 retrocopies	retro_itri_1065, retro_itri_1383, retro_itri_1737, retro_itri_296,
Tupaia belangeri	ENSTBEG00000015944	1 retrocopy	retro_tbel_4315,
Tarsius syrichta	ENSTSYG00000002196	7 retrocopies	retro_tsyr_1053, retro_tsyr_1559, retro_tsyr_165, retro_tsyr_1695, retro_tsyr_1874, retro_tsyr_448, retro_tsyr_943,
Tursiops truncatus	ENSTTRG00000013614	1 retrocopy	retro_ttru_1448,