RetrogeneDB ID: retro_mmul_1172

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:109850466..109850957(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB28
• Ensembl ID: ENSMMUG00000022025
• Aliases: None
• Description: ras-related protein Rab-28 [Source:RefSeq peptide;Acc:NP_001252653]

Sequence

>retro_mmul_1172
ATAACATTGCCAGGAAACTTGAAGGTTACTCTTCAAGTATGAGACGTAGGGGGTGTGTACAATAGGCAGCAAGATGGTGG
GTACATTTATCTGTGGACCACAGAGAATCCTCTTGATACATGATGTTACAAATTAGCAAAGCTTGGAGAATTTAAAAGAT
CGGTACATTGTACTGAAGAAAGGGAGGGAAGAGTCAGAAACTTTGCTACTGGTTGCCTTGGTGAGCAATAAAATTGATTT
GGAGCATATGGAAACAGTAAAACCTGAAAAACACTTATGGGTTTGCCAGGAAAACGGTTTTAGTAGCCACTTTATCTCAG
CCAAGACAGGAGACTGTATCTTCCTGTATTTTCAGAAAGTTGCTAATGAAATCCTTGGAATCAAATTAAAGCAGAAAAAT
AGAAGAGTCACAGAGGGTGGTGAAGGCAGATATTAGAAACTACAACCAGGCCCCTAGAACTGTTACTCTTCCTACAAGTT
CTGTGTCTGCA

Alignment

ORF - retro_mmul_1172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.1 %
• Parental protein coverage: 75.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ITLPGNLNVTLQIWDIGGQ-TIGGKMLDKYIYGAQGVLLVYDITNYQSFENLEDWYTVVKKVSEESETQP
          ITLPGNL.VTLQ..D.GG..TIG.KM....I.G.Q..LL..D.TN.QS.ENL.D.Y.V.KK..EESET..
Retrocopy ITLPGNLKVTLQV*DVGGV>TIGSKMVGTFICGPQRILLIHDVTN*QSLENLKDRYIVLKKGREESETLL

Parental  LVALVGNKIDLEHMRTIKPEKHLRFCQENGFSSHFVSAKTGDSVFL-CFQKVAAEILGIKLNKAEIEQSQ
          LVALV.NKIDLEHM.T.KPEKHL..CQENGFSSHF.SAKTGD..FL..F.K.....L........IE.SQ
Retrocopy LVALVSNKIDLEHMETVKPEKHLWVCQENGFSSHFISAKTGDCIFL>IFRKLLMKSLESN*SR-KIEESQ

Parental  RVVKADIVNYNQEPMSRTVNPPRSSMCA
          RVVKADI.NYNQ.P..RTV..P.SS..A
Retrocopy RVVKADIRNYNQAP--RTVTLPTSSVSA

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	18.82 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	16.58 RPM
SRP007412_cerebellum	0.00 RPM	15.69 RPM
SRP007412_heart	0.12 RPM	6.65 RPM
SRP007412_kidney	0.00 RPM	11.27 RPM
SRP007412_liver	0.00 RPM	1.94 RPM
SRP007412_testis	0.04 RPM	65.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1172 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1172 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009344	1 retrocopy	retro_amel_469,
Choloepus hoffmanni	ENSCHOG00000001523	1 retrocopy	retro_chof_1365,
Callithrix jacchus	ENSCJAG00000012136	2 retrocopies	retro_cjac_2713, retro_cjac_4126,
Dasypus novemcinctus	ENSDNOG00000007750	4 retrocopies	retro_dnov_1426, retro_dnov_1771, retro_dnov_2419, retro_dnov_381,
Dipodomys ordii	ENSDORG00000012378	1 retrocopy	retro_dord_682,
Homo sapiens	ENSG00000157869	7 retrocopies	retro_hsap_4166, retro_hsap_4259, retro_hsap_4261, retro_hsap_4263, retro_hsap_4265, retro_hsap_4317, retro_hsap_4762,
Gorilla gorilla	ENSGGOG00000024190	1 retrocopy	retro_ggor_2966,
Macropus eugenii	ENSMEUG00000006792	4 retrocopies	retro_meug_1079, retro_meug_1182, retro_meug_1510, retro_meug_913,
Macaca mulatta	ENSMMUG00000022025	1 retrocopy	retro_mmul_1172 ,
Nomascus leucogenys	ENSNLEG00000016243	1 retrocopy	retro_nleu_2292,
Pongo abelii	ENSPPYG00000014610	1 retrocopy	retro_pabe_3707,
Pan troglodytes	ENSPTRG00000015920	2 retrocopies	retro_ptro_2893, retro_ptro_3171,
Rattus norvegicus	ENSRNOG00000017074	1 retrocopy	retro_rnor_1075,
Sarcophilus harrisii	ENSSHAG00000009274	1 retrocopy	retro_shar_602,
Sus scrofa	ENSSSCG00000022358	2 retrocopies	retro_sscr_482, retro_sscr_514,
Ictidomys tridecemlineatus	ENSSTOG00000004135	1 retrocopy	retro_itri_27,
Tarsius syrichta	ENSTSYG00000010939	2 retrocopies	retro_tsyr_1450, retro_tsyr_1750,
Tursiops truncatus	ENSTTRG00000003622	1 retrocopy	retro_ttru_697,