RetrogeneDB ID: retro_mmul_1483

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:169346614..169347394(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3922
• Ensembl ID: ENSMMUG00000018095
• Aliases: None
• Description: eukaryotic translation initiation factor 2 subunit 2 [Source:RefSeq peptide;Acc:NP_001253795]

Sequence

>retro_mmul_1483
ATGATTTTTTATCTTACTATGAGCAAGAAGAAAAAGAAGAAGAAACCTTTTATGTTAGATGAGGAAGGGGATACCCAAAC
AGAGGAAACCCAGCCTTCAGAAACAAAAGAAGTGGAGCCAGAGCCAACTGAGGACAAAGATTTGGAAGCTGATGAAGAGG
ACACTAGGAAAAAAGATGCTTCTGATGATCTAGATGACTTGAACTTCTTTAATCAAAAGAAAAAGAAGAAAAAAACTAAA
AAGGTATTTGATATTGATGAAGCTGAAGAAGGTGTAAAGGATCTTAAGATTGAAAGTGATGTTCAAGAACCAACTGAACC
AGAGGATGACCTTGACATTATGCTTGGCAATAACAAGAAGAAAAAGGAGAATGTTAAGTTCCCAGATAAGGATGAAATAT
TAGAGAAAGATGAAGCTCTAGAAGATGAAGACAGCAAAAAAGATGATGGTATCTCATTCAGTAATCAGACAGGCCCTACT
TGGGCAGGCTCAGAAAGAGACTACACATAGGAGGAGCTGCTGAATCGAGTGTTCAACATGATGAGAGAAAAGAATCCAGA
TATGGTTGCTGGGAAGAAAAGGAAATTTGTCATGAAACCTCCACAGGTTGTCCATGTAGGAACCAAGAAAACTTCTTTTG
TCAACTTTACAGATATCTGTAAACTATTACATCGTCAGCCCAAACATCTCCTTGCATTTTTGTTGGCTGAATTGGGTACA
AGTGGTTCTATAGATGGTAATAACCAACTTGTAATCAAAGGAAGATTCCAACAGAAACAG

Alignment

ORF - retro_mmul_1483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.42 %
• Parental protein coverage: 78.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIFDPTMSKKKKKKKKPFMLDEEGDTQTEETQPSETKEVEPEPTEDKDLEADEEDTRKKDASDDLDDLNF
          MIF..TMSKKKKKKK.PFMLDEEGDTQTEETQPSETKEVEPEPTEDKDLEADEEDTRKKDASDDLDDLNF
Retrocopy MIFYLTMSKKKKKKK-PFMLDEEGDTQTEETQPSETKEVEPEPTEDKDLEADEEDTRKKDASDDLDDLNF

Parental  FNQKKKKKKTKKIFDIDEAEEGV---KIESDVQEPTEPEDDLDIMLGNKKKKKKNVKFPDEDEILEKDEA
          FN...........FDIDEAEEGV...KIESDVQEPTEPEDDLDIMLGN.KKKK.NVKFPD.DEILEKDEA
Retrocopy FNXXXXXXXXXXVFDIDEAEEGVKDLKIESDVQEPTEPEDDLDIMLGNNKKKKENVKFPDKDEILEKDEA

Parental  LEDEDSKKDDGISFSNQTGPAWAGSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVVRVGTK
          LEDEDSKKDDGISFSNQTGP.WAGSERDYT.EELLNRVFN.MREKNPDMVAG.KRKFVMKPPQVV.VGTK
Retrocopy LEDEDSKKDDGISFSNQTGPTWAGSERDYT*EELLNRVFNMMREKNPDMVAGKKRKFVMKPPQVVHVGTK

Parental  KTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQ
          KTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQ
Retrocopy KTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQ

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	0.67 RPM	42.24 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	41.41 RPM
SRP007412_cerebellum	1.36 RPM	33.13 RPM
SRP007412_heart	1.59 RPM	32.74 RPM
SRP007412_kidney	0.94 RPM	37.44 RPM
SRP007412_liver	0.16 RPM	29.29 RPM
SRP007412_testis	0.75 RPM	23.29 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1483 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1483 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1483 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196, retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101,
Homo sapiens	ENSG00000125977	3 retrocopies	retro_hsap_2176, retro_hsap_2260, retro_hsap_713,
Gorilla gorilla	ENSGGOG00000015546	5 retrocopies	retro_ggor_1683, retro_ggor_1726, retro_ggor_2007, retro_ggor_280, retro_ggor_604,
Microcebus murinus	ENSMICG00000006944	1 retrocopy	retro_mmur_1583,
Macaca mulatta	ENSMMUG00000018095	1 retrocopy	retro_mmul_1483 ,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Nomascus leucogenys	ENSNLEG00000010034	2 retrocopies	retro_nleu_2242, retro_nleu_466,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Pan troglodytes	ENSPTRG00000013412	2 retrocopies	retro_ptro_1600, retro_ptro_508,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,