RetrogeneDB ID: retro_mmul_1457

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:114603317..114604083(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4082
• Ensembl ID: ENSMMUG00000017045
• Aliases: None
• Description: basic leucine zipper and W2 domain-containing protein 2 [Source:RefSeq peptide;Acc:NP_001181788]

Sequence

>retro_mmul_1457
CTAATGACATCCATTCTTAATAGCCTTTATAATGAGAATTTGGTTAAAGAAGGGGTTTCAGCAGCTTTTGCTGTAAAGCT
CTTTAAATCATGAATAAATGAAAAAGATATCAATGCAGTAGCTTCAAGTCTTCGGAAAGTCAGCATGGATAATAGCCTGA
TGGAACTTCTTCCCGCCAATAAGCAAAGCATTAAACACTTCACAAAGTATTTTACTGAGGCAGGCTTGAAAGAGCTTTCG
GAATATGTTCGGAATTAGCAATCCATCAGAGCTTGTAAGGAGCTCCAGAAAGAACTTCAAGAACAGATGTCCCGTGGTGA
TCCATTTAAGGATATAATTTTATATGTCAAGGAGGAGATGAAAAAAAACCAACTTCCCAGAACCAGTTGTCATCAAAACA
GTCTGGTCAAATGTAATGAGGTCTGTGGAATGCAACAAAAAAGAGGAGCTTGTAGCACAGCAAACTGTCAAGCATTTGAA
GCAATACAGCACTCTACTTGCCGCCTTTACTACTCAAGGTCAGTCTGAGCCGACTCTGTAACTGAAGATTCAGGAGTATT
GCTATGACAACATTCATTTCATGAAAGCCTTCCAGAAAATAGTGGTGCTTTTTTATAAAGCTGTAATCTTGAGCGAAGAG
CCCATTTTGAAGTGGTATAAAGGTACACATGTTGCAAAGGGGAAGAGTGTTTTCCTTGAGCAAATGAGAAAGTTTGGAGA
GTGGTTCAAAAATCCTGAAGAAGGATCTGAATCTGAAGCTGAAGAA

Alignment

ORF - retro_mmul_1457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.45 %
• Parental protein coverage: 60.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPATILTSLFTDSLVKEGIAASFAVKLFKAWMAEKDANSVTSSLRKANLDKRLLELFPVNRQSVDHFAKY
          L...IL.SL....LVKEG..A.FAVKLFK....EKD.N.V.SSLRK...D..L.EL.P.N.QS..HF.KY
Retrocopy LMTSILNSLYNENLVKEGVSAAFAVKLFKS*INEKDINAVASSLRKVSMDNSLMELLPANKQSIKHFTKY

Parental  FTDAGLKELSDFLRVQQSLGTRKELQKELQERLSQECPIKEVVLYVKEEMKRNDLPETA-VIGLLWTCIM
          FT.AGLKELS...R..QS....KELQKELQE..S...P.K...LYVKEEM....LP.T..VI...W...M
Retrocopy FTEAGLKELSEYVRN*QSIRACKELQKELQEQMSRGDPFKDIILYVKEEMXXXQLPRTS>VIKTVWSNVM

Parental  NAVEWNKKEELVAEQALKHLKQYAPLLAVFSSQGQSELILLQKVQEYCYDNIHFMKAFQKIVVLFYKADV
          ..VE.NKKEELVA.Q..KHLKQY..LLA.F..QGQSE..L..K.QEYCYDNIHFMKAFQKIVVLFYKA..
Retrocopy RSVECNKKEELVAQQTVKHLKQYSTLLAAFTTQGQSEPTL*LKIQEYCYDNIHFMKAFQKIVVLFYKAVI

Parental  LSEEAILKWYKEAHVAKGKSVFLDQMKKFVEWLQNAEEESESEGEE
          LSEE.ILKWYK..HVAKGKSVFL.QM.KF.EW..N.EE.SESE.EE
Retrocopy LSEEPILKWYKGTHVAKGKSVFLEQMRKFGEWFKNPEEGSESEAEE

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	15.46 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.52 RPM
SRP007412_cerebellum	0.00 RPM	8.33 RPM
SRP007412_heart	0.00 RPM	98.22 RPM
SRP007412_kidney	0.00 RPM	27.46 RPM
SRP007412_liver	0.00 RPM	7.64 RPM
SRP007412_testis	0.04 RPM	3.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1457 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1457 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1457 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2881
Pan troglodytes	retro_ptro_1949
Gorilla gorilla	retro_ggor_1997

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001663	4 retrocopies	retro_dnov_2177, retro_dnov_2422, retro_dnov_2649, retro_dnov_575,
Equus caballus	ENSECAG00000022038	1 retrocopy	retro_ecab_1121,
Macaca mulatta	ENSMMUG00000017045	1 retrocopy	retro_mmul_1457 ,
Ochotona princeps	ENSOPRG00000005256	2 retrocopies	retro_opri_665, retro_opri_9,
Pongo abelii	ENSPPYG00000017763	1 retrocopy	retro_pabe_2385,
Pteropus vampyrus	ENSPVAG00000014571	1 retrocopy	retro_pvam_481,
Ictidomys tridecemlineatus	ENSSTOG00000002506	1 retrocopy	retro_itri_1286,
Tarsius syrichta	ENSTSYG00000009806	1 retrocopy	retro_tsyr_1923,
Tursiops truncatus	ENSTTRG00000009867	1 retrocopy	retro_ttru_162,