RetrogeneDB ID: retro_mmul_1964

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:100165430..100165965(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000006011
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.4339
• Ensembl ID: ENSMMUG00000021075
• Aliases: None
• Description: None

Sequence

>retro_mmul_1964
TCTGTATGTGAAACTTGCCTACTGATCAGTTACACAACCAATGCATTTCCTGGAGAATATATCCCTACTGTCTTTGACAA
TTATTCTGCCAATGTTATGGTAGATAGAAAACCAGTGAATCTGGGCTCATGGGATACAGCTGCTCAAGAAGATTATGACA
GATCATGCCGCCTATCCTATCCTCAAACAGATGTGTTCTTAATTTGCTTTTCCCTTGTGAGTCCTGCATCATTTGAAAAT
GTCCGTGCAAAGTGGTATCCTGAGGTGCGGCACCACCGTCCCAACACTCCCATCATCCTAGTGGGAACTAAACTTGAACT
TAGGGATGATAAAGACACGATCGAGAAACTGAAGAAGAAGCTGACTCCCATCACCTATCTGCAGGGTCTAGCTATAGCTA
AGGAGACTGGTGCTGTAAAATACCTGGAGTGCTTGGCGTTCACACAGTGAGGCCTCAACAGTGTTAGACGAAGAGATTCA
AGCAGTCCTCTGCCCACCTCCCGTGAAGAAGAGGAAGAGAAAATGCTTGCTGTTG

Alignment

ORF - retro_mmul_1964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICF
          .V..TCLLISYTTNAFPGEYIPTVFDNYSANVMVD.KPVNLG.WDTA.QEDYDR...LSYPQTDVFLICF
Retrocopy SVCETCLLISYTTNAFPGEYIPTVFDNYSANVMVDRKPVNLGSWDTAAQEDYDRSCRLSYPQTDVFLICF

Parental  SLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAV
          SLVSPASFENVRAKWYPEVRHH.PNTPIILVGTKL.LRDDKDTIEKLK.KKLTPITY.QGLA.AKE.GAV
Retrocopy SLVSPASFENVRAKWYPEVRHHRPNTPIILVGTKLELRDDKDTIEKLK-KKLTPITYLQGLAIAKETGAV

Parental  KYLECSALTQRGLKTV-FDEAIRAVLCPPPVKKRKRKCLLL
          KYLEC.A.TQ.GL..V...E.......PP.VKKRKRKCLLL
Retrocopy KYLECLAFTQ*GLNSV>DEEIQAVLCPPP-VKKRKRKCLLL

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	250.10 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	187.62 RPM
SRP007412_cerebellum	0.13 RPM	177.26 RPM
SRP007412_heart	0.00 RPM	88.62 RPM
SRP007412_kidney	0.00 RPM	125.94 RPM
SRP007412_liver	0.00 RPM	73.03 RPM
SRP007412_testis	0.08 RPM	39.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1964 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1964 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1964 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3072
Gorilla gorilla	retro_ggor_2110
Pongo abelii	retro_pabe_2546

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009233	2 retrocopies	retro_btau_1601, retro_btau_332,
Canis familiaris	ENSCAFG00000015716	1 retrocopy	retro_cfam_496,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Macaca mulatta	ENSMMUG00000018854	2 retrocopies	retro_mmul_1346, retro_mmul_210,
Macaca mulatta	ENSMMUG00000021075	4 retrocopies	retro_mmul_1310, retro_mmul_1964 , retro_mmul_2642, retro_mmul_721,
Macaca mulatta	ENSMMUG00000022009	8 retrocopies	retro_mmul_1449, retro_mmul_1612, retro_mmul_1685, retro_mmul_1900, retro_mmul_1932, retro_mmul_24, retro_mmul_349, retro_mmul_598,
Oryctolagus cuniculus	ENSOCUG00000009956	1 retrocopy	retro_ocun_305,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,