RetrogeneDB ID: retro_mmul_1572

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:87575627..87575977(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4156
• Ensembl ID: ENSMMUG00000017375
• Aliases: None
• Description: UMP-CMP kinase [Source:RefSeq peptide;Acc:NP_001180547]

Sequence

>retro_mmul_1572
GAAATGGATCAGACAATGGCTGCCAATGCTACGAATAAATTCTTGATTGATGAATTTCTAAGAAATCAAGACAACCTTCA
AGGTTGGGCCAAGAGCATGGATGAGAAAGGCAGATGTGCATCTGGTTCTGTTTTCTGACCATAATATTGAGATCTGCATC
AAAGCATGTCTTGAGAGGAGGGAACAGTGGTAAGAGTGAAGACAGCAGAGAGAGCTTGGGAAAGAGAATTCAGATCCATC
TTCAAGTTAACAAAAACAATTACTGACTCATACGAAGAAATCGGGAAAGTCAATAAAACAGATGCTTCTAAACCTGTCCA
TGAAGTTTTTCTGAAGTTGTGAAAAATTTC

Alignment

ORF - retro_mmul_1572 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.85 %
• Parental protein coverage: 51.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EMDQTMAANAQKNKFLIDGFPRNQDNLQGWNKTMD-GKADVSFVLFFDCNNEICIERCLER-GKSSGRSD
          EMDQTMAANA..NKFLID.F.RNQDNLQGW.K.MD..KADV..VLF.D.N.EICI..CLER.G.S.G.S.
Retrocopy EMDQTMAANAT-NKFLIDEFLRNQDNLQGWAKSMD>RKADVHLVLFSDHNIEICIKACLER>GNS-GKSE

Parental  DNRESLEKRIQTYLQ-STKPIIDLYEEMGKVKKIDASKSVDEV-FDEVVQIF
          D.RESL.KRIQ..LQ..TK.I.D.YEE.GKV.K.DASK.V.EV.F.EVV..F
Retrocopy DSRESLGKRIQIHLQ>LTKTITDSYEEIGKVNKTDASKPVHEV<FSEVVKNF

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	19.72 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	15.31 RPM
SRP007412_cerebellum	0.26 RPM	23.38 RPM
SRP007412_heart	0.06 RPM	14.90 RPM
SRP007412_kidney	0.23 RPM	21.71 RPM
SRP007412_liver	0.04 RPM	14.92 RPM
SRP007412_testis	0.04 RPM	4.22 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1572 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1572 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1572 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000012	2 retrocopies	retro_amel_1074, retro_amel_1711,
Canis familiaris	ENSCAFG00000004030	1 retrocopy	retro_cfam_1729,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609, retro_chof_840,
Callithrix jacchus	ENSCJAG00000021250	2 retrocopies	retro_cjac_2652, retro_cjac_2992,
Cavia porcellus	ENSCPOG00000014747	4 retrocopies	retro_cpor_1070, retro_cpor_1295, retro_cpor_417, retro_cpor_799,
Felis catus	ENSFCAG00000025426	1 retrocopy	retro_fcat_1259,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572 , retro_mmul_66,
Mustela putorius furo	ENSMPUG00000012394	1 retrocopy	retro_mputfur_1061,
Mus musculus	ENSMUSG00000028719	1 retrocopy	retro_mmus_2576,
Otolemur garnettii	ENSOGAG00000026904	2 retrocopies	retro_ogar_1589, retro_ogar_3204,
Pongo abelii	ENSPPYG00000001380	1 retrocopy	retro_pabe_1369,
Rattus norvegicus	ENSRNOG00000007775	1 retrocopy	retro_rnor_1940,
Sorex araneus	ENSSARG00000009745	2 retrocopies	retro_sara_199, retro_sara_294,
Sus scrofa	ENSSSCG00000003885	1 retrocopy	retro_sscr_454,
Tupaia belangeri	ENSTBEG00000017494	2 retrocopies	retro_tbel_3597, retro_tbel_691,
Tarsius syrichta	ENSTSYG00000007511	1 retrocopy	retro_tsyr_319,
Vicugna pacos	ENSVPAG00000004127	2 retrocopies	retro_vpac_345, retro_vpac_373,