RetrogeneDB ID: retro_mmul_54

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:48865863..48866385(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000005015
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAD1
• Ensembl ID: ENSMMUG00000030184
• Aliases: None
• Description: cell cycle checkpoint protein RAD1 [Source:RefSeq peptide;Acc:NP_001248089]

Sequence

>retro_mmul_54
ATGTGTTACCAAGGTTATGGTTACCCTTTGAGGCTGTTTCTGGAAGAAGGAGGAGTGGTAACAGTCTGCAAAATCAATAC
ACAGGACCCTGAGGACACCTTGGATTTTGATTTCTGCAGCACCAATGTTATTAATAAAATTATTCTGCAGTCAGAGGGGC
TCCGTGAAGCATTTTCTGAATTGGATATGATGAGCGAAGTCCTACAAATTACAATGTCTCTTGACAAGCCTTATTTCAGG
TTATCTACTTTTGGAAATGCACGAAGTTCCCACCTTGACTATCCCAAAGATTCTGATTTGATGGAAGCATTTCATTGTAA
TCAAATCCAAGTCAACAGATACAAGATTTCTTTACTGAAACCCTCTACAAAGGCATTAGTCCTATCTTGTAAGGTATCTA
TTCGGACAGATAACAGAGGTTTCCTTTCATCACAGTATATGATTAGAAATGAAGATGGACAAATATGTTTTGTGGAATAT
TACTGCTGCCCTGATGAAGAAGTTCCTGAGTCTGAGTCTTGA

Alignment

ORF - retro_mmul_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCYQGYGYPLMLFLEEGGVVTVCKINTQEPEETLDFDFCSTNVINKIILQSEGLREAFSELDMTSEVLQI
          MCYQGYGYPL.LFLEEGGVVTVCKINTQ.PE.TLDFDFCSTNVINKIILQSEGLREAFSELDM.SEVLQI
Retrocopy MCYQGYGYPLRLFLEEGGVVTVCKINTQDPEDTLDFDFCSTNVINKIILQSEGLREAFSELDMMSEVLQI

Parental  TMSPDKPYFRLSTFGNAGSSHLDYPKDSDLMEAFHCNQTQVNRYKISLLKPSTKALVLSCKVSIRTDNRG
          TMS.DKPYFRLSTFGNA.SSHLDYPKDSDLMEAFHCNQ.QVNRYKISLLKPSTKALVLSCKVSIRTDNRG
Retrocopy TMSLDKPYFRLSTFGNARSSHLDYPKDSDLMEAFHCNQIQVNRYKISLLKPSTKALVLSCKVSIRTDNRG

Parental  FLSLQYMIRNEDGQICFVEYYCCPDEEVPES
          FLS.QYMIRNEDGQICFVEYYCCPDEEVPES
Retrocopy FLSSQYMIRNEDGQICFVEYYCCPDEEVPES

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	5.71 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.84 RPM
SRP007412_cerebellum	0.19 RPM	5.81 RPM
SRP007412_heart	0.06 RPM	2.18 RPM
SRP007412_kidney	0.00 RPM	3.99 RPM
SRP007412_liver	0.00 RPM	1.58 RPM
SRP007412_testis	0.08 RPM	6.29 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_54 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_54 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_54 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018514	1 retrocopy	retro_cjac_1004,
Homo sapiens	ENSG00000113456	1 retrocopy	retro_hsap_634,
Gorilla gorilla	ENSGGOG00000004219	1 retrocopy	retro_ggor_555,
Macaca mulatta	ENSMMUG00000030184	1 retrocopy	retro_mmul_54 ,
Nomascus leucogenys	ENSNLEG00000014437	1 retrocopy	retro_nleu_455,
Otolemur garnettii	ENSOGAG00000014822	2 retrocopies	retro_ogar_2296, retro_ogar_2726,
Pongo abelii	ENSPPYG00000015389	1 retrocopy	retro_pabe_564,
Pan troglodytes	ENSPTRG00000016783	1 retrocopy	retro_ptro_462,
Tarsius syrichta	ENSTSYG00000002894	1 retrocopy	retro_tsyr_738,