RetrogeneDB ID: retro_mmul_455

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:201452798..201453174(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000004439
• Aliases: None
• Description: None

Sequence

>retro_mmul_455
AGTCCCTGGATGGTCACCAGATCCGCGTGGATCATGCAGGCAAGTCTGCTGCGGAACCAGAGGAGGTGCTTTTGGGACCC
ATGGGCATGGTCGCAGCTACTCTAGAAGTGGTGGGAACCAGGACTATGGGAGTGGCAGGTGTGACAGTTGACCTGGAGGA
TATAGATATGGATATGGACAGTCCAGCTACTATAATGTCAGAAACCAGGGTAGTTATGAATGCTACTCAGAAGGAATTAC
AGAGGCAGTTATGACAACTGAAATGATACATGTGCACATAATATACACAAGGAATAGCTCTTCTGATCCAGGATCATCCT
TCCAAAAGGCTGTATTTATAAAGGTTTTTCGAGCTGCATGGAAACATTTTATTTTA

Alignment

ORF - retro_mmul_455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.19 %
• Parental protein coverage: 76.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPWMVVRSVWIMQASLL-GEPEEVALGPMGVVAATLEVVGTRAMGVAGIMTVDLEGMDMDMDVPETIMAE
          SPWMV.RS.WIMQASLL..EPEEV.LGPMG.VAATLEVVGTR.MGVAG..TVDLE..DMDMD.P.TIM.E
Retrocopy SPWMVTRSAWIMQASLL<AEPEEVLLGPMGMVAATLEVVGTRTMGVAGV-TVDLEDIDMDMDSPATIMSE

Parental  TRVVMTATQEE-ITETIMTTEMRHAHNVDTQGIISDPGSSFQMAVFIKVFGAALKHLIL
          TRVVM.ATQ.E.ITE..MTTEM.H.H...T....SDPGSSFQ.AVFIKVF.AA.KH.IL
Retrocopy TRVVMNATQKE<ITEAVMTTEMIHVHIIYTRNSSSDPGSSFQKAVFIKVFRAAWKHFIL

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	0.45 RPM	29.36 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	24.59 RPM
SRP007412_cerebellum	0.32 RPM	32.29 RPM
SRP007412_heart	0.29 RPM	30.74 RPM
SRP007412_kidney	0.59 RPM	31.10 RPM
SRP007412_liver	0.00 RPM	21.34 RPM
SRP007412_testis	1.73 RPM	18.70 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_455 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_455 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002320	1 retrocopy	retro_cjac_2655,
Echinops telfairi	ENSETEG00000001939	6 retrocopies	retro_etel_1057, retro_etel_1060, retro_etel_1209, retro_etel_1476, retro_etel_169, retro_etel_531,
Microcebus murinus	ENSMICG00000014371	5 retrocopies	retro_mmur_1450, retro_mmur_878, retro_mmur_957, retro_mmur_958, retro_mmur_998,
Macaca mulatta	ENSMMUG00000004439	1 retrocopy	retro_mmul_455 ,
Sorex araneus	ENSSARG00000003340	1 retrocopy	retro_sara_45,
Tupaia belangeri	ENSTBEG00000003499	10 retrocopies	retro_tbel_100, retro_tbel_1589, retro_tbel_1774, retro_tbel_1779, retro_tbel_1869, retro_tbel_2829, retro_tbel_3822, retro_tbel_3999, retro_tbel_4268, retro_tbel_427,