RetrogeneDB ID: retro_mmul_1590

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:73521678..73522104(-)
• Located in intron of: ENSMMUG00000001561

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2420
• Ensembl ID: ENSMMUG00000000193
• Aliases: None
• Description: eukaryotic translation initiation factor 1A, X-chromosomal [Source:RefSeq peptide;Acc:NP_001248706]

Sequence

>retro_mmul_1590
AAGAATAAAGGTAAAGGAGGTAAAAACAGGCGCAGGGGTAAAAATGAGAATGAATCTGAAAAAAGAGAGCTGGTGTTTAA
AGAGGATGGACAAGAGTATGCTCAGGTAATCAAAATGTTGGGAAATGGACAATTGGAAGCACTGTGTTTTGATGGTGTAA
AGAGGTTATGCCATATCAGAGGGAAATTGAGAAAAAAGGTTTGGATAAATACTTCAGACATTATATTGGTTGGTCTACGA
GACTATCAGGATAACAAAACTGATGTAATTTTAAAGTACAATGCAGATGAAGCTAGAAGCCTGAAGGTATATGGCGAGCT
TCCAGAGCATGCTAAAATCAATGAAACAGACACATTTGGTCCTGGAGATGATGATGAAATCCAATTTGATGATATTGGAG
ATGACGATGAAGACATTGATGATATC

Alignment

ORF - retro_mmul_1590 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPSGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVWIN
          K..GKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNG.LEA.CFDGVKRLCHIRGKLRKKVWIN
Retrocopy KNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGQLEALCFDGVKRLCHIRGKLRKKVWIN

Parental  TSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDEDID
          TSDIILVGLRDYQDNK.DVILKYNADEARSLK.YGELPEHAKINETDTFGPGDDDEIQFDDIGDDDEDID
Retrocopy TSDIILVGLRDYQDNKTDVILKYNADEARSLKVYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDEDID

Parental  DV
          D.
Retrocopy DI

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	3.03 RPM	28.57 RPM
SRP007412_brain_prefrontal_cortex	6.19 RPM	18.01 RPM
SRP007412_cerebellum	5.17 RPM	26.73 RPM
SRP007412_heart	9.36 RPM	27.68 RPM
SRP007412_kidney	6.69 RPM	21.01 RPM
SRP007412_liver	3.48 RPM	8.63 RPM
SRP007412_testis	4.07 RPM	25.41 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1590 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1590 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1590 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016604	1 retrocopy	retro_amel_1421,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Latimeria chalumnae	ENSLACG00000015565	1 retrocopy	retro_lcha_65,
Macaca mulatta	ENSMMUG00000000193	1 retrocopy	retro_mmul_1590 ,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,