RetrogeneDB ID: retro_mmul_718

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214742455:33543..34308(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.778
• Ensembl ID: ENSMMUG00000005871
• Aliases: None
• Description: eukaryotic peptide chain release factor subunit 1 [Source:RefSeq peptide;Acc:NP_001253403]

Sequence

>retro_mmul_718
ATGGTGGACGACCCCAGTGCTGCCGACAGGAAGGTGGAGATCTGGAAGATGAAGAAGCTCAGTAAAAGCCTGGAGGTGGC
CCGCGGCAATGGCACCAGCATGATATCACTGATTATCCCTCCTAAAGACCAGATTTCACGAGTGTCAAAAATGTTAGCAG
ATGAGTTTGGATCTGCATCTAACATTAAGTCACAAGTAAACTGCCTTTCAGTCCTGGGAGCCATTACATCTGTACAACAA
AGACTCAGACATTATAACAAAGTACCTCCAAATAGTCTGGTTGTTTACTGTGGAACAATAGTAACAGAAGGAGGAAAGGA
AAAGAAAGTTAACGTTGATTTTGAACCTTTCAAACCAATTAATACGTCATACTATTTGTGTGACAACAAAATCCATACAG
AGGCTCTTACAGCACTAATTTCAGATGACAGCAAGTTTGGATTCATTGTAATAGATGGTAGTGGTGCACTTTTTGGCACA
CTCCAAGGAAACACAAAAGAAGTCCTGCAAAAATTCACTGTGGATCTCCCAAAGAAACACGGTAGAGGAGGTCAGTCAGC
CTTGTGTTTTGCCCGTTTAAGAATGGAAAAGCGATCTAACAATGTTCAGAAAGTAGCAGAGAACGCTGTGCAGGTGTTTA
TTTCTGGGGACGAAGGGAAGATTGCTAGTCTAGTTTTAGCTGGATCCACTGACTTTAAAACTGAACTAAATCACTATGAT
ATGTTTGATCAGAGGTTACAATCGAAAGTTTTAAAATTAGTTGAT

Alignment

ORF - retro_mmul_718 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 58.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADDPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLS
          M.DDPSAADR.VEIWK.KKL.KSLE.ARGNGTSMISLIIPPKDQISRV.KMLADEFG.ASNIKS.VN.LS
Retrocopy MVDDPSAADRKVEIWKMKKLSKSLEVARGNGTSMISLIIPPKDQISRVSKMLADEFGSASNIKSQVNCLS

Parental  VLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALL
          VLGAITSVQQRL..YNKVPPN.LVVYCGTIVTE.GKEKKVN.DFEPFKPINTS.YLCDNK.HTEALTAL.
Retrocopy VLGAITSVQQRLRHYNKVPPNSLVVYCGTIVTEGGKEKKVNVDFEPFKPINTSYYLCDNKIHTEALTALI

Parental  SDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAETAV
          SDDSKFGFIVIDGSGALFGTLQGNT.EVL.KFTVDLPKKHGRGGQSAL.FARLRMEKR.N.V.KVAE.AV
Retrocopy SDDSKFGFIVIDGSGALFGTLQGNTKEVLQKFTVDLPKKHGRGGQSALCFARLRMEKRSNNVQKVAENAV

Parental  QLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVD
          Q.FISGD....A.LVLAGS.DFKTEL...DMFDQRLQSKVLKLVD
Retrocopy QVFISGDEGKIASLVLAGSTDFKTELNHYDMFDQRLQSKVLKLVD

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	67.12 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	53.07 RPM
SRP007412_cerebellum	0.06 RPM	56.44 RPM
SRP007412_heart	0.00 RPM	79.08 RPM
SRP007412_kidney	0.23 RPM	75.70 RPM
SRP007412_liver	0.12 RPM	34.00 RPM
SRP007412_testis	0.38 RPM	107.61 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_718 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_718 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001282	1 retrocopy	retro_cfam_99,
Callithrix jacchus	ENSCJAG00000006776	2 retrocopies	retro_cjac_2316, retro_cjac_4133,
Dasypus novemcinctus	ENSDNOG00000010830	3 retrocopies	retro_dnov_1925, retro_dnov_2504, retro_dnov_610,
Equus caballus	ENSECAG00000013041	1 retrocopy	retro_ecab_740,
Echinops telfairi	ENSETEG00000007362	2 retrocopies	retro_etel_1237, retro_etel_1400,
Gorilla gorilla	ENSGGOG00000000657	4 retrocopies	retro_ggor_2326, retro_ggor_2561, retro_ggor_2562, retro_ggor_2919,
Macaca mulatta	ENSMMUG00000005871	2 retrocopies	retro_mmul_1658, retro_mmul_718 ,
Mustela putorius furo	ENSMPUG00000009338	1 retrocopy	retro_mputfur_1448,
Oryctolagus cuniculus	ENSOCUG00000006650	3 retrocopies	retro_ocun_1188, retro_ocun_1614, retro_ocun_462,
Rattus norvegicus	ENSRNOG00000019450	1 retrocopy	retro_rnor_2935,