RetrogeneDB ID: retro_mmul_154

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:33320809..33321151(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000019505
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.12923
• Ensembl ID: ENSMMUG00000017704
• Aliases: None
• Description: eukaryotic translation initiation factor 1b [Source:RefSeq peptide;Acc:NP_001244814]

Sequence

>retro_mmul_154
ATGTCCGCTATCCAGAACCTCCACTCTTTCGACCCCTTTGCTGATGCAAGTAAGGGTGATGACCTGCTTCCTGCTGGCAC
TGAGGATTATATCCATATAAGAATTCAACAGAGAAACGGCAGGAAGACCCTTACTACTGTCCAAGGGATCGCTGATGATT
ACGATAAAAAGAAACTAGTGAAGGCGTTTAAGAAGAAGTTTGCCTGCAATGGTACTGTAATTGAGCATCCAGAATATGGA
GAAGTAATTCAGCTACAGGGTGACCAACGCAAGAACATATGCCAGTTCCTCGTAGAGATTGGACTGGCTAAGGACGATCA
GCTGAAGGTTCATGGGTTTTAA

Alignment

ORF - retro_mmul_154 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTIQNLQSFDPFADATKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACN
          MS.IQNL.SFDPFADA.KGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACN
Retrocopy MSAIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACN

Parental  GTVIEHPEYGEVIQLQGDQRKNICQFLLEVGIVKEEQLKVHGF
          GTVIEHPEYGEVIQLQGDQRKNICQFL.E.G..K..QLKVHGF
Retrocopy GTVIEHPEYGEVIQLQGDQRKNICQFLVEIGLAKDDQLKVHGF

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	35.07 RPM	37.65 RPM
SRP007412_brain_prefrontal_cortex	89.64 RPM	32.68 RPM
SRP007412_cerebellum	55.53 RPM	26.09 RPM
SRP007412_heart	43.58 RPM	62.71 RPM
SRP007412_kidney	53.17 RPM	19.37 RPM
SRP007412_liver	38.67 RPM	6.65 RPM
SRP007412_testis	59.44 RPM	33.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_154 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_154 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013689	4 retrocopies	retro_dord_179, retro_dord_307, retro_dord_626, retro_dord_669,
Echinops telfairi	ENSETEG00000017295	5 retrocopies	retro_etel_1228, retro_etel_1480, retro_etel_1793, retro_etel_31, retro_etel_4,
Microcebus murinus	ENSMICG00000013223	5 retrocopies	retro_mmur_254, retro_mmur_445, retro_mmur_535, retro_mmur_654, retro_mmur_706,
Macaca mulatta	ENSMMUG00000017704	1 retrocopy	retro_mmul_154 ,
Monodelphis domestica	ENSMODG00000011056	2 retrocopies	retro_mdom_1113, retro_mdom_1382,
Mus musculus	ENSMUSG00000006941	1 retrocopy	retro_mmus_587,
Otolemur garnettii	ENSOGAG00000025224	1 retrocopy	retro_ogar_1943,
Ictidomys tridecemlineatus	ENSSTOG00000012168	1 retrocopy	retro_itri_1597,
Tupaia belangeri	ENSTBEG00000013185	6 retrocopies	retro_tbel_1861, retro_tbel_1920, retro_tbel_1996, retro_tbel_2954, retro_tbel_3209, retro_tbel_3867,
Tarsius syrichta	ENSTSYG00000006338	3 retrocopies	retro_tsyr_1574, retro_tsyr_2154, retro_tsyr_888,