RetrogeneDB ID: retro_mmul_1658

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:188453014..188454123(+)
• Located in intron of: ENSMMUG00000006250

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_1658
GTAAACCACCATTGAGTCCTGGGAGCCATTACATCTATACAACAAAGGCTCAAACTGTATAACAAAGTACCTCCAGATGG
TCTGGTTGTTTACTGTGGAACAACTGTAACGGAAGAAGGAAAGGAAAAAAAAGAAAGTCAACATTGACTTTGAATCTTTC
AAACAAAATTAATACGTCATTGTATTTGTGTGACAACAAATTCCATGCTGGGGCTCTTACAGCACTACTTTCAGACTATA
GCAAGTTTGGATTCGTTGTAATAGATGCAAGTGTGCACTTTTTGGCACACTCCAAGGAAACATTAAGAGAAGTCCTGCAC
AAATTCACTGTGGATCTCCCAGAGAAACACAGTAGAGGAGGATAGTTAGGCTTGCGTTTTGCCCGTTTAAAAATGGAAAA
GCGACATAACTATGTTCAGAAAGTAGCGGAGACTGCTGTGCAGCTGTTTATTTCTGGGGACAAAGTGAATGTGGCTGGTC
TAGTTTTAGCTGGATCCGCTGACTTTGAACTAAATCAATCTGGTGTGTTTGATCAGAGGTTACAATAGAAAGTTTTAAAA
TTAGTTGTTATATCCTACGGTGGTGAAAATGGATTCAACCAGGCTACTAAGTTATCTACTGAAGTCCTCTCCAAAGTGAA
ATTCATTCAAGAGAAGAAATCAATAGAACGATACTTTGATGAAATCACCCAGGACACGCCCAAGTACTGTTTTGGGGTTG
AAGATACACTAAAGGCTTTGGAAATGGGAGCTGTAGAAATTCTAATGGTCCATGAAAATCTGGATATAATGACATTATGT
TCTTCATTGCCAAGGCACAGAAGAGAAAATTCTCTAACTCCAGACCAAGAAAAGGATAAATCTCATTTCACAGACAAAGA
GACTGGACAGGAACATGAACTTATCGAGAGCACGCCCCTGTTGGAATGGTTTGCTAACAACTATAAAAAATGTGGAGCGA
CATTGGAAATTGTCACAGATAAAACGCAAGAAGGGTCTTGGTTTGTGAAAGGATCTGGTGGAATTGGAGGTATCCCGCGG
TACGGAGTAGACTTCCAGGGAATGGAATACCAAGGAGGAGACAATGAATTTTTTGACCTTGATGATTAC

Alignment

ORF - retro_mmul_1658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.53 %
• Parental protein coverage: 85.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCG-TIVTE-EGKEKKVNIDFEPFKP-INTSLYLCDNKFH
          VN...VLGAITS.QQRLKLYNKVPP.GLVVYCG.T...E.E....KVNIDFE.FK..INTSLYLCDNKFH
Retrocopy VNHH*VLGAITSIQQRLKLYNKVPPDGLVVYCGTTVTEE>ERXXXKVNIDFESFKQ>INTSLYLCDNKFH

Parental  TEALTALLSDDSKFGFIVIDGSG-ALFGTLQGNT-REVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHN
          ..ALTALLSD.SKFGF.VID.S..ALFGTLQGN..REVLHKFTVDLP.KH.RGG...LRFARL.MEKRHN
Retrocopy AGALTALLSDYSKFGFVVIDASV<ALFGTLQGNI>REVLHKFTVDLPEKHSRGG*LGLRFARLKMEKRHN

Parental  YVRKVAETAVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENGFNQAIEL
          YV.KVAETAVQLFISGDKVNVAGLVLAGSADF..EL.QS..FDQRLQ.KVLKLV.ISYGGENGFNQA..L
Retrocopy YVQKVAETAVQLFISGDKVNVAGLVLAGSADF--ELNQSGVFDQRLQ*KVLKLVVISYGGENGFNQATKL

Parental  STEVLSNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIM-RYVLHCQGTE
          STEVLS.VKFIQEKK.I.RYFDEI.QDT.KYCFGVEDTLKALEMGAVEIL.V.ENLDIM..YVLHCQGTE
Retrocopy STEVLSKVKFIQEKKSIERYFDEITQDTPKYCFGVEDTLKALEMGAVEILMVHENLDIM>HYVLHCQGTE

Parental  E-EKILYLTPEQEKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGG
          E.E..L....E..K..SHFTDKETGQEHELIES.PLLEWFANNYKK.GATLEIVTDK.QEGS.FVKG.GG
Retrocopy E<ENSLTPDQEKDK--SHFTDKETGQEHELIESTPLLEWFANNYKKCGATLEIVTDKTQEGSWFVKGSGG

Parental  IGGILRYRVDFQGMEYQGGDDEFFDLDDY
          IGGI.RY.VDFQGMEYQGGD.EFFDLDDY
Retrocopy IGGIPRYGVDFQGMEYQGGDNEFFDLDDY

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	0.34 RPM	67.12 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	53.07 RPM
SRP007412_cerebellum	0.58 RPM	56.44 RPM
SRP007412_heart	0.29 RPM	79.08 RPM
SRP007412_kidney	0.35 RPM	75.70 RPM
SRP007412_liver	0.24 RPM	34.00 RPM
SRP007412_testis	0.11 RPM	107.61 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1658 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1658 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1658 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,