RetrogeneDB ID: retro_mmul_1733

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:156419404..156419977(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3I
• Ensembl ID: ENSMMUG00000006119
• Aliases: EIF3I, EIF3S2
• Description: None

Sequence

>retro_mmul_1733
CTCAGAACTGATGTAGCTGTCCAGACCTGTGGCAAGGACTTTGGAAACAATATCGCTATATTCTCTACAGACAAGCAGAT
GGGCTACCAGTGCTTTGTGAGCTTCTTTTATCTGCAGGACCTAAGCCAGATTGACGGCAATGAGACATACATGAAAATTC
TTTACAATGACTGTAATATCACCAGTGCTTTGTGAGGACTCCCCAGGGGAGTGCATCAACACAGGCCATAAGAGTGGAGT
GTCCAACCAGTATAATGCCAAGTCTGGAGAGGTATTGGTGAGTGTTAAATAGCACTCCAAGGAGATCAGTGACATCCAGT
TATCCAGGGACATGACCAAGTTCATCACTGCAACCAAGGACAAGACAGCCAAGTTCTTTGATTCTACAACTCTTGAACAT
CAAGAGATTTTCTGGACAGAACATCTCATCAACTCAGCTGCCCTTTCCCCAATTATAGTGACCATGTGATACTGGGTAAC
AGACAGAAAGCCATGGATGTAACTGCAACCTCCAACAGGACTGGCAGGTTTGAGCCCAGGTTCTTCCATCTGGCCTTTGA
AAAAGAGTTTGGA

Alignment

ORF - retro_mmul_1733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.98 %
• Parental protein coverage: 59.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKTNSAVRTCGFDFGGNIIMFSTDKQMGYQCFVSFFDLRDPSQIDNNEPYMKIPCNDSKITSAVWG-PLG
          L.T..AV.TCG.DFG.NI..FSTDKQMGYQCFVSFF.L.D.SQID.NE.YMKI..ND..ITSA..G...G
Retrocopy LRTDVAVQTCGKDFGNNIAIFSTDKQMGYQCFVSFFYLQDLSQIDGNETYMKILYNDCNITSAL*G>SPG

Parental  ECIIAGHESGELNQYSAKSGEVLVNVKEHSRQINDIQLSRDMTMFVTASKDNTAKLFDSTTLEHQKTFRT
          ECI..GH.SG..NQY.AKSGEVLV.VK.HS..I.DIQLSRDMT.F.TA.KD.TAK.FDSTTLEHQ..F.T
Retrocopy ECINTGHKSGVSNQYNAKSGEVLVSVK*HSKEISDIQLSRDMTKFITATKDKTAKFFDSTTLEHQEIFWT

Parental  ERPVNSAALS-PNY-DHVVLGGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFG
          E...NSAALS.PNY.DHV.LG..Q.AMDVT.TS.R.G.FE.RFFHLAFE.EFG
Retrocopy EHLINSAALS<PNYSDHVILGNRQKAMDVTATSNRTGRFEPRFFHLAFEKEFG

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	0.00 RPM	43.03 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	47.99 RPM
SRP007412_cerebellum	0.00 RPM	33.64 RPM
SRP007412_heart	0.00 RPM	36.98 RPM
SRP007412_kidney	0.00 RPM	58.10 RPM
SRP007412_liver	0.00 RPM	50.31 RPM
SRP007412_testis	0.00 RPM	23.45 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1733 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1733 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1733 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3894
Pongo abelii	retro_pabe_3175

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010674	1 retrocopy	retro_cfam_321,
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497,
Homo sapiens	ENSG00000084623	2 retrocopies	retro_hsap_3888, retro_hsap_3894,
Gorilla gorilla	ENSGGOG00000001579	3 retrocopies	retro_ggor_2540, retro_ggor_2615, retro_ggor_2623,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073,
Macaca mulatta	ENSMMUG00000006119	2 retrocopies	retro_mmul_1730, retro_mmul_1733 ,
Macaca mulatta	ENSMMUG00000013307	2 retrocopies	retro_mmul_1695, retro_mmul_985,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822,
Nomascus leucogenys	ENSNLEG00000002426	2 retrocopies	retro_nleu_1129, retro_nleu_1135,
Pongo abelii	ENSPPYG00000001598	2 retrocopies	retro_pabe_3169, retro_pabe_3175,