RetrogeneDB ID: retro_mmul_2604

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:83647726..83648284(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP9
• Ensembl ID: ENSMMUG00000004146
• Aliases: None
• Description: putative hydrolase RBBP9 [Source:RefSeq peptide;Acc:NP_001247700]

Sequence

>retro_mmul_2604
ATGGCTTCTCCTAGCAAGGCAGTGATTGTTCCCGGGAATGGAGGCGGGGATGTGACCACCCACGGCTGGTATGGCTGGGT
GAAAAAGGAGCTGGAGAAGATACCTGGTTTCCAGTGTTTGGCTAAAAACATGCCCGACCCAGTTACAGCATGAGAGAGCA
TCTGGTTGCCCTTCATGGAGACAGAGCTGCACTGTGATGAGAAGACCATCATTATCGGCCACGGTTCTAGGGCCATCGCA
GCCATGAGGTATGCAGAAACACATCGAGTATATGCTATTGTATTAGTGTCTGCGTACACATCAGACTTGGGGGATGAAAA
TGAGCGTGCAAGTGGATACTTCACCCGCCCCTGGCAGTGGGAGAAGATCAAGGCCAACTGCCCTTACGTTGTGCAGTTTG
GCTCCACTGACGACCCATTCCTTCCCTGGAAGGAACAACAAGAAGTGGCCGATAGGTTGGAAACCAAATTGCACAAATTC
ACTGACCGTGGCCACTTTCAGAACACAGAGTTTCATGAACTGATTACTGTGGTAAAGTCTTTGCTGAAAGTACCAGCA

Alignment

ORF - retro_mmul_2604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASPSKAVIVPGNGGGDVTTHGWYGWVKKELEKIPGFQCLAKNMPDPITARESIWLPFMETELHCDEKTI
          MASPSKAVIVPGNGGGDVTTHGWYGWVKKELEKIPGFQCLAKNMPDP.TA.ESIWLPFMETELHCDEKTI
Retrocopy MASPSKAVIVPGNGGGDVTTHGWYGWVKKELEKIPGFQCLAKNMPDPVTA*ESIWLPFMETELHCDEKTI

Parental  IIGHSSGAIAAMRYAETHRVYAIVLVSAYTSDLGDENERASGYFTRPWQWEKIKANCPYIVQFGSTDDPF
          IIGH.S.AIAAMRYAETHRVYAIVLVSAYTSDLGDENERASGYFTRPWQWEKIKANCPY.VQFGSTDDPF
Retrocopy IIGHGSRAIAAMRYAETHRVYAIVLVSAYTSDLGDENERASGYFTRPWQWEKIKANCPYVVQFGSTDDPF

Parental  LPWKEQQEVADRLETKLHKFTDRGHFQNTEFHELITVVKSLLKVPA
          LPWKEQQEVADRLETKLHKFTDRGHFQNTEFHELITVVKSLLKVPA
Retrocopy LPWKEQQEVADRLETKLHKFTDRGHFQNTEFHELITVVKSLLKVPA

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	0.11 RPM	1.34 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.43 RPM
SRP007412_cerebellum	0.00 RPM	0.58 RPM
SRP007412_heart	0.00 RPM	0.71 RPM
SRP007412_kidney	0.00 RPM	2.58 RPM
SRP007412_liver	0.00 RPM	2.49 RPM
SRP007412_testis	0.00 RPM	1.43 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2604 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2604 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013286	1 retrocopy	retro_chof_1398,
Callithrix jacchus	ENSCJAG00000005170	1 retrocopy	retro_cjac_768,
Macaca mulatta	ENSMMUG00000004146	1 retrocopy	retro_mmul_2604 ,
Rattus norvegicus	ENSRNOG00000007972	1 retrocopy	retro_rnor_1118,