RetrogeneDB ID: retro_mmul_1582

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:56454127..56454792(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000019896
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.1680
• Ensembl ID: ENSMMUG00000003695
• Aliases: None
• Description: None

Sequence

>retro_mmul_1582
ATGCTAGAACCACAGGAGAATGGCATGATTGACCTACCAGATTATGAGCATGTAGAAGATGAAGCTTTTCGTCCTTTCCC
ACCTGCAGTCTCTCCAGACAGACAAGATGATGAAGAGGCGGAACCTGATGAAGAGTCAGGAAGTGGAGCACCTGTTCCTG
TACCTCCAAAGAGAACAGTTAAAAGAAATATACCCAAGCTGGATGCTAGAGATTAATTTCAGAGAGAGGACTTCCAGCCT
TAAGGCATGTATTTGATAAGGCAAAATTCAAAGGTAAAGGTCATGAGGCTGAAGATTTGAAGACCCTAATCAGACACATG
GAACACTGGGCACGTAGGCTATTCCCTAAACTGCAGTTTGAGGATTGTATTGACAGAGTTGAATACCTGGGAAATGAAAA
AGAAGTTCAGACTTATTTAAAACAAATTCGACTTGATCTCCCTATTTTACCTGAAGATTTTATTAGCAATAACGATGAAG
TTGTGGAAAATAATGGACATGATGTAACTGCTACTGAATTAGATCCCTTTCTGACAAAGTCATCTGAAAGTGAGATGTTT
GCTTCTGAGTCAAGTAGAAGCCTAACAGAAGAGCAACAACAAAAAATTGAGAGAAATAAACAACTGACCTTAGAAAGAAG
GCAGGCAAAGCTGCTAAGTAATAGT

Alignment

ORF - retro_mmul_1582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.34 %
• Parental protein coverage: 72.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLEPQENGMIDLPDYEHVEDETFPPFPPPASPERQDGEGIEPDEESGSGALVPVPPKRTVKRNIPKLDAQ
          MLEPQENGMIDLPDYEHVEDE.F.PFPP..SP.RQD.E..EPDEESGSGA.VPVPPKRTVKRNIPKLDA.
Retrocopy MLEPQENGMIDLPDYEHVEDEAFRPFPPAVSPDRQDDEEAEPDEESGSGAPVPVPPKRTVKRNIPKLDAR

Parental  -RLISERGLPALRHVFDKAKFKGKGHEAEDLKMLIRHMEHWAHRLFPKLQFEDFIDRVEYLGSKKEVQTC
          .RLISERGLPALRHVFDKAKFKGKGHEAEDLK.LIRHMEHWA.RLFPKLQFED.IDRVEYLG..KEVQT.
Retrocopy <RLISERGLPALRHVFDKAKFKGKGHEAEDLKTLIRHMEHWARRLFPKLQFEDCIDRVEYLGNEKEVQTY

Parental  LKRIRLDLPILHEDFVSNNDEVAENNEHDVTATELDPFLTNSSESEIFASESSRSLTEEQQQRIERNKQL
          LK.IRLDLPIL.EDF.SNNDEV.ENN.HDVTATELDPFLT.SSESE.FASESSRSLTEEQQQ.IERNKQL
Retrocopy LKQIRLDLPILPEDFISNNDEVVENNGHDVTATELDPFLTKSSESEMFASESSRSLTEEQQQKIERNKQL

Parental  ALERRQAKLLSNS
          .LERRQAKLLSNS
Retrocopy TLERRQAKLLSNS

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	2.35 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.24 RPM
SRP007412_cerebellum	0.00 RPM	2.20 RPM
SRP007412_heart	0.00 RPM	1.12 RPM
SRP007412_kidney	0.00 RPM	1.53 RPM
SRP007412_liver	0.00 RPM	0.83 RPM
SRP007412_testis	0.04 RPM	7.35 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1582 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1582 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1582 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1145

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004860	1 retrocopy	retro_chof_223,
Dasypus novemcinctus	ENSDNOG00000003177	3 retrocopies	retro_dnov_1334, retro_dnov_1481, retro_dnov_410,
Homo sapiens	ENSG00000075131	1 retrocopy	retro_hsap_4837,
Gorilla gorilla	ENSGGOG00000000061	3 retrocopies	retro_ggor_1268, retro_ggor_2907, retro_ggor_3016,
Loxodonta africana	ENSLAFG00000026016	1 retrocopy	retro_lafr_1104,
Microcebus murinus	ENSMICG00000004386	2 retrocopies	retro_mmur_155, retro_mmur_255,
Macaca mulatta	ENSMMUG00000003695	1 retrocopy	retro_mmul_1582 ,
Nomascus leucogenys	ENSNLEG00000012909	1 retrocopy	retro_nleu_1336,
Pan troglodytes	ENSPTRG00000007192	2 retrocopies	retro_ptro_1145, retro_ptro_3220,
Rattus norvegicus	ENSRNOG00000043068	1 retrocopy	retro_rnor_364,