RetrogeneDB ID: retro_mmul_1075

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:78220721..78221708(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2789
• Ensembl ID: ENSMMUG00000002821
• Aliases: ORC3, ORC3L
• Description: None

Sequence

>retro_mmul_1075
GAAAAGCAAGTTGCGCTCTTGACCAATGAGAGATGTTTGAAGGAGGAAACACAATTATTACTAGAAAACCTTCATGTGTA
TCATAGGAATTACTTCCCGGTTTTGAGATGTCTTCATAAGTTCACCTCTTCTCTTCCCAAGTATCCACAAGGTTGACAGA
TCAGAGAGTTGTACCGCACATGTTTAGAAAAGAACATACGGAATTCAGAGGAGTATGCATCAGTCTTATAGCTGCTGAAG
ATGTTGGCAAACGATGAACTGATGACCATACTTGAGGAATGTTTCAAGGTTTTTAAATCTTCTTGTGAAAATCACCTTGG
CAGCACAGCTAAGAGAATAGAGAAGTTCCTGGCCCAGTTTCAGAGCTTCGATGAAACCAAAGAGGAAGAAGATGCTTCTG
GGTCAGTCAAAGAGGCTTCAGAAGACAGACCTCTATCATCTTCAGAAGTCTTTACAGGAAATGAAGGAGTCAAGTGGAAG
TAAGAAGCAAACCAAATTTGAAGTACTCAGAGAAAATATTGTGAACTTCATGACTGTCTAGTGAGAGAACAGCTTCTGCC
TCCTGAGACACAGCCTCTCCATGAGGTGGTCCGCTTCAGTGCTGCCCATGCCCTTCGTGAGCATTTAGATGCTGCTCCAT
GAATTGCCCTCCATACTGCACTCAACAATCCTTACTATTATCTAAAGAATGAAGCACTGAAAAGCAAAGAAGGGTGCATT
CCAAATATCACCCAAGACATCTGCATAGCATATAAATTGCACCTAGAGTGTTGCAGGCTAATCAACCTTGTGTACTGTTC
ATAGGCTTTTGCAACAGTTTTGACAGCTGCTGAAAAAATGGATGCAAATTCTGCAACCTCAGAAGAAATGAATGAAATTA
TCCATGCTTGGTTTATTAGAACTTTTTTTGAACTAGAACTTTTAGGATTTATAAAATCTACCAAATAGAAGACTGACCTT
GTGGCAAGGCTAACATGGGGAGGCTGC

Alignment

ORF - retro_mmul_1075 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.08 %
• Parental protein coverage: 50.69 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKQVALLTNERCLKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYPLGRQIRELYCTCLEKNIWDSE
          EKQVALLTNERCLKEETQLLLENLHVYH.NYF.VLRCLHKFTSSLPKYP.G.QIRELY.TCLEKNI..SE
Retrocopy EKQVALLTNERCLKEETQLLLENLHVYHRNYFPVLRCLHKFTSSLPKYPQG*QIRELYRTCLEKNIRNSE

Parental  EYASVLQLLRMLAKDELMTILEKCFKVFKSSCEKHLGSTAKRIEEFLAQFQSLDAENKEEEDASGS-QPK
          EYASVL.LL.MLA.DELMTILE.CFKVFKSSCE.HLGSTAKRIE.FLAQFQS.D.....EE......Q.K
Retrocopy EYASVL*LLKMLANDELMTILEECFKVFKSSCENHLGSTAKRIEKFLAQFQSFD--ETKEEEDASG>QSK

Parental  GLQKTDLYHLQKSLLEMKELRRSKKQTKFEVLRENAVNFI-DCLVREYLLPPETQPLHEVVYFSAAHALR
          .LQKTDLYHLQKSL.EMKE...SKKQTKFEVLREN.VNF..DCLVRE.LLPPETQPLHEVV.FSAAHALR
Retrocopy RLQKTDLYHLQKSLQEMKESSGSKKQTKFEVLRENIVNFM<DCLVREQLLPPETQPLHEVVRFSAAHALR

Parental  EHLNAAPRIALHTALNNPYYYLKNEALKSEEGCIPNIAPDICIAYKLHLECSRLINLVDWSEAFATVVTA
          EHL.AAP.IALHTALNNPYYYLKNEALKS.EGCIPNI..DICIAYKLHLEC.RLINLV..S.AFATV.TA
Retrocopy EHLDAAP*IALHTALNNPYYYLKNEALKSKEGCIPNITQDICIAYKLHLECCRLINLVYCS*AFATVLTA

Parental  AEKMDANSATSEEMNEIIHARFIRAVSELELLGFIKPTKQKTDHVARLTWGGC
          AEKMDANSATSEEMNEIIHA.FIR...ELELLGFIK.TK.KTD.VARLTWGGC
Retrocopy AEKMDANSATSEEMNEIIHAWFIRTFFELELLGFIKSTK*KTDLVARLTWGGC

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	10.98 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	9.44 RPM
SRP007412_cerebellum	0.00 RPM	15.50 RPM
SRP007412_heart	0.00 RPM	8.07 RPM
SRP007412_kidney	0.35 RPM	8.22 RPM
SRP007412_liver	0.00 RPM	2.61 RPM
SRP007412_testis	1.55 RPM	29.10 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1075 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1075 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1075 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_913

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000730	1 retrocopy	retro_cjac_913,
Homo sapiens	ENSG00000135336	1 retrocopy	retro_hsap_798,
Macaca mulatta	ENSMMUG00000002821	1 retrocopy	retro_mmul_1075 ,
Nomascus leucogenys	ENSNLEG00000012990	1 retrocopy	retro_nleu_413,
Pongo abelii	ENSPPYG00000016830	1 retrocopy	retro_pabe_712,
Pan troglodytes	ENSPTRG00000018408	1 retrocopy	retro_ptro_555,