RetrogeneDB ID: retro_mmul_430

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:150038669..150039613(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000007790
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.4101
• Ensembl ID: ENSMMUG00000001856
• Aliases: None
• Description: None

Sequence

>retro_mmul_430
GTCATGTTGTTCACCAAGGAAGACAACCCCCAAGGCAATGACAGTGTCAAAGCCAGCTGGGCCAGGACCAAAGCCAATAA
CCACTGAGATACAGGCATCTTCCTTGACTTGATGCACCTGAAGAAACCTGGAGGCTTTGACATATCTTTGTTTTACAGAG
ATATCATCAGCATAGCAGAGGATGAGGACCTCAGGGCTCCCTTTGAGGAATCCAGCAAGCTAGAAGACCTGTTGAGGCAG
TTTTGAGCCAAGGAGATCAGGAAGTGAGCACTCAGCAGGTTAAAGTTGAAGTTTAGCAAAGATATAGTGCTCTCTGTGGG
CATTTATAATCTGATCCAGAAGGCTCTCAAGCCTCCTCCAATAAAACTCTATCGAGAAATAGATGAATCAGTGAAAACTA
AGACCTGGACATGTAATATAAATACAGGCAGTTTGCTTCTGCCTAGAGATACCACGAGGTCTCAGATGTATGGAAGGCAT
CAGATTATACTGGAGAAAGAGGAAACAGAAGAGCTAAAATAGTTTGATGAACCAGGTTTGATTCTCATGGGTTTAAGCCC
TTGGTAAAGCTGAAGAAGCACCATTATCCAAGGCCCTCCTTCTTTGTGTACTCTGAGGAGTCGCTGATGAATGGGAGCTC
AACCCTGTTCAGTGCTCTACTCATCATGTGTCTGGAGAAGGAGGTCACAGCATTGTGCAGATACACACCCTGCAGGAACA
TCCCCCCTTATTTTGTGGCTTTGGTGCCACAGGAAGAGGAGTTGGATGATCAGAAAATTCAGGTGACTCCTGCAGGAATC
CAGCTGGTCTTTTTATGCTATGCTGATAATAAAGGGAAGGTGCCCTTTACTAAAAAAGCCACGGCAACCCCAGAGCAGGT
GGACAAGGTGAAGGCTATTGTTCAGAAGCTCCGATTCAAATACAGAAGTGACAGCTTTGAGAAC

Alignment

ORF - retro_mmul_430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 56.35 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEE
          .MLFT.EDNP.GNDS.KAS.ARTKA....DTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLR..FEE
Retrocopy VMLFTKEDNPQGNDSVKASWARTKANNH*DTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRAPFEE

Parental  SSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGVYNLVQKALKPPPIKLYRETNEPVKTKTRTFNT
          SSKLEDLLR...AKE.RK.ALSRLKLK..KDIV.SVG.YNL.QKALKPPPIKLYRE..E.VKTKT.T.N.
Retrocopy SSKLEDLLRQF*AKEIRK*ALSRLKLKFSKDIVLSVGIYNLIQKALKPPPIKLYREIDESVKTKTWTCNI

Parental  STGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLM-GFKPLVLLKKHHYLRPSLFVYPEESL
          .TG.LLLP.DT.RSQ.YG..QIILEKEETEELK.FD.PGL.LM.GFKPLV.LKKHHY.RPS.FVY.EESL
Retrocopy NTGSLLLPRDTTRSQMYGRHQIILEKEETEELK*FDEPGLILM<GFKPLVKLKKHHYPRPSFFVYSEESL

Parental  VIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQDEELDDQKIQVTPPGFQLVFLPFADDKR
          ..GSSTLFSALLI.CLEKEV.ALCRYTP.RNIPPYFVALVPQ.EELDDQKIQVTP.G.QLVFL..AD.K.
Retrocopy MNGSSTLFSALLIMCLEKEVTALCRYTPCRNIPPYFVALVPQEEELDDQKIQVTPAGIQLVFLCYADNKG

Parental  KMPFTEKIMATPEQVDKMKAIVEKLRFTYRSDSFEN
          K.PFT.K..ATPEQVDK.KAIV.KLRF.YRSDSFEN
Retrocopy KVPFTKKATATPEQVDKVKAIVQKLRFKYRSDSFEN

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	179.50 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	156.91 RPM
SRP007412_cerebellum	0.00 RPM	173.32 RPM
SRP007412_heart	0.00 RPM	126.37 RPM
SRP007412_kidney	0.00 RPM	164.55 RPM
SRP007412_liver	0.00 RPM	112.73 RPM
SRP007412_testis	0.00 RPM	388.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_430 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_430 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_430 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000196419	4 retrocopies	retro_hsap_4066, retro_hsap_4880, retro_hsap_4913, retro_hsap_511,
Gorilla gorilla	ENSGGOG00000015885	2 retrocopies	retro_ggor_3067, retro_ggor_471,
Macaca mulatta	ENSMMUG00000001856	2 retrocopies	retro_mmul_2346, retro_mmul_430 ,
Nomascus leucogenys	ENSNLEG00000015610	3 retrocopies	retro_nleu_1552, retro_nleu_2287, retro_nleu_2676,
Pongo abelii	ENSPPYG00000011876	1 retrocopy	retro_pabe_3821,
Tupaia belangeri	ENSTBEG00000011736	3 retrocopies	retro_tbel_1474, retro_tbel_1523, retro_tbel_3859,
Tursiops truncatus	ENSTTRG00000006749	1 retrocopy	retro_ttru_289,