RetrogeneDB ID: retro_mmul_1862

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:145402107..145402676(-)
• Located in intron of: ENSMMUG00000022184

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000019164
• Aliases: None
• Description: None

Sequence

>retro_mmul_1862
ATGAACGGAGACAGCATGTTTGCAAAGAGACCCAAGGATGATGCTCAGATATCAGAGAAGAGACACAAACAAGGCCTTCA
ATGATACTGCCAGATACTTATCTAAGAAAGAGTGGGAAAAGCTGAAAAACTCACAGAAAATCACCTATGTGTATATGAAG
AGAAACTATGAGACCATGACTAAACTAGGTCTCTAGGCCACCCTCCCACCTTTCATGTACAATAAATGAGCCGCAGAATT
CCAGGGAATGACTTTGATACAGACTAAAACTGTGGGAATCAGGATGAACATCCTCAGATGGCTTTCGGTATGCTACATGG
AAACTTTCGAAAGATGATGCCCAAGAAGCCAGCAGAGGAAGGAAATGATTTGAAGGGAGTGCCAGAAGCATCTGGCTCAC
GAAGCAATGGGAAACAGCTGTGTCCCCCGGGAAAAGAAAGTACCTCTGAGAAGACTAATAAGACATCTGGACCCAAGAAA
AGTGGGAATATGTCTGGATCCACAGACTGCAAGAGAGAAAGTATCTAATGATTTATAAAGAGATCAGCGACCCTGAGGAA
GATGATGAA

Alignment

ORF - retro_mmul_1862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNGDDAFARR-PRVGAQIPEK-IQKAFDDIAKYFSKKEWERMKVSEKIVYVYKKRKYEAMSKLGFKVTLP
          MNGD..FA.R.PR...........KAF.D.A.Y.SKKEWE..K.S.KI.YVY.KR.YE.M.KLG...TLP
Retrocopy MNGDSMFAKR>PRMMLRYQRRDTNKAFNDTARYLSKKEWEKLKNSQKITYVYMKRNYETMTKLGL*ATLP

Parental  PFMRNKRATDFQG-NDSDNDPNHGNQVEHPQMTSGRLQGIFPKIMPEKPAEEGNDSKGVPEASGPQNDVK
          PFM.NK.A..FQG.ND.D.D.N.GNQ.EHPQM..G.L.G.F.K.MP.KPAEEGND.KGVPEASG.....K
Retrocopy PFMYNK*AAEFQG<NDFDTD*NCGNQDEHPQMAFGMLHGNFRKMMPKKPAEEGNDLKGVPEASGSRSNGK

Parental  QLCPPGKPSTSEKINKRSGP-KTG-KHAWTHRLRERKQLVIYEEISDPEEDDE
          QLCPPGK.STSEK.NK.SGP.K.G....W.HRL.ERK.L.IY.EISDPEEDDE
Retrocopy QLCPPGKESTSEKTNKTSGPKKSG<EYVWIHRLQERKYLMIYKEISDPEEDDE

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	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.39 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.12 RPM	0.00 RPM
SRP007412_liver	0.04 RPM	0.00 RPM
SRP007412_testis	0.11 RPM	0.98 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1862 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1862 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3512
Pan troglodytes	retro_ptro_2385
Gorilla gorilla	retro_ggor_2374
Pongo abelii	retro_pabe_2903
Callithrix jacchus	retro_cjac_2373

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014776	1 retrocopy	retro_cjac_2373,
Macaca mulatta	ENSMMUG00000019164	1 retrocopy	retro_mmul_1862 ,
Pongo abelii	ENSPPYG00000020365	1 retrocopy	retro_pabe_2903,
Ictidomys tridecemlineatus	ENSSTOG00000015375	3 retrocopies	retro_itri_1394, retro_itri_1855, retro_itri_746,