RetrogeneDB ID: retro_mmul_2589

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:64623683..64625502(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9577
• Ensembl ID: ENSMMUG00000001062
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:RefSeq peptide;Acc:NP_001182737]

Sequence

>retro_mmul_2589
TCAGCGAAAAAGAAGAAGAAGAAGGGGAAGACTATCTTCCTAACAGACTTTCTGGCTGAGGATGGGAGGACTGGTAGAGG
AAGCACCTATGTTTCCAAACCAGTCCCCTGGGCTGATGAAACAGATGACCTGGAAGGAGATGTTTCAACAACTTGGCACA
GTAGTGATGATGATGTGTATAGGTCACCTTCAATTGACCGTTCCATCCTTCCCACTGCTCCACGGGCTACTCGGGAACCC
AATATTGACCAGAGCCGTCTTCCTAAATCACCACCCTACACTGCTTTTCTAGGGAACCTATCCTATGATATGACAGAAGA
ATCAATTAAGGAACTCTTTTGAGGATTAAATATCAGTGCAGTGCCTTTACCACGTGAACCCAGCAATCCAGAGAGGTTGA
AAGGTTTTGATTATGCTGAAATTGAGGACCTGGATTCCCTGCTCAGTTCCATGAGTCTCAATGAAGAGTCTCTAGGTAAC
AGGAAAATTCAAGTGGACGTTGCTGATCAAGCACAGGGGAAAGACAGGGAGGATCGTTCTTTTGGCCATGATAGAAAGCG
GGATTCTGACAAAACAGATACAGACTGGAGGACTCCTCCTGCCACAGACAGCTTTGATGACTACCTGCCTAGAAGAGGTG
ATAATAGCTTTGGAGACTAGTATCGAGATCGTTGTGATTCAGACCGGTATCACGATGGGTATCGGCATGGGTAACGGTAT
GGCCCACACTGGGATATGGATTGATACGGCAGCCGGGATGGCTATGTTGACCGAGGCAGCAGAGACTATGATAGAGGCTA
TGATTCTCGGATAGGCAGTGGCAGAAGAGCATTTGACAGTGGGTGCGGCAGAGATGATGACTACAGAGGAGGCAGGAATG
GCTATGAAGACCTATACGACAGATAGGATGATCAGTCATGGAGCTCCAGAGATGATTACTCTCGGGATGATTATATGCGT
GATGATAGAGGTCTCTCCCAAAGACCCAAACTGAATCTAAAGCCTCGGAGTACTCCTAAGGAAGATGATTCCTCTGCTAG
TACCTCCCAGTGCAGTCAAGGTGCTTCTATCTTTGGAGGGGCAAAGCACGTTGACACAGCTACTAGAGAAAGAGAAGTAG
AAGAACAGCTACAGAAGGAACACGAGAAGTTGCAGCGTTAGCTGGATGAGCCAAAACTAGAACGACAGCCTCGAGAGAGA
CACCCAAGCTGGCAAAGTGAAGAAACTCGGGAACGGGAACAGTCGAGGACAGGAAGTGAGTCATCGCAGACTGGGACCTC
CGCCACATCCGGCAGAAATGCACGAAGGAGAGAGAGAAGTCACTAGAAAATGAAACACTCAATAAGGAGGAAGATTGTCA
GTCTCTAACTTCTAAACCTCCCAAACCTGATAAGCCCCTAAAGGTAACGCCAGCCCCTTCACCAAAGGAGAATGGTTGGG
TGAAGTGAAGTTCTAAACCTCCTGCTCAATCTCAGAGCTCAGACACAGAGCAGCAATCCCCTACAACTGGTGGGGTAAAG
TAGCTCCAGCTCAACCATCTGAGTAAGGACCAGCAAGGAAAGATGAAAAGGAAGTAGATGGGATGAATGTCCCAAAAGGC
CAAACTGGGAACTCTAGCCATGGTCCAGGAGAGGGAGGGAACAAAGACCACTGGAAGGAGTCAGATAGGAAAGATGGCAA
AAAGGATAAAGACTCCAGATCTGCACCTGAGTCAAAAAAACCTGAGGAAAATCCAGCTTCCAAGTTCAGTTCTGCAAGGA
AGTGTGCTGCTCTCTCCATTGACGGTGAAGATGAAAACGAGGGAGATGATTAAGCCGAA

Alignment

ORF - retro_mmul_2589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.26 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRSIL
          .AKKK.KKGKTI.LTDFLAEDG.TG.GSTYVSKPV.WADETDDLEGDVSTTWHS.DDDVYR.P.IDRSIL
Retrocopy SAKKKKKKGKTIFLTDFLAEDGRTGRGSTYVSKPVPWADETDDLEGDVSTTWHSSDDDVYRSPSIDRSIL

Parental  PTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAE
          PTAPRA.REPNID.SRLPKSPPYTAFLGNL.YD.TEESIKE.F.GLNISAV.LPREPSNPERLKGF.YAE
Retrocopy PTAPRATREPNIDQSRLPKSPPYTAFLGNLSYDMTEESIKELF*GLNISAVPLPREPSNPERLKGFDYAE

Parental  FEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDDYPP
          .EDLDSLLS..SLNEESLGNR.I.VDVADQAQ.KDR.DRSFG.DR.RDSDKTDTDWR..PATDSFDDY.P
Retrocopy IEDLDSLLSSMSLNEESLGNRKIQVDVADQAQGKDREDRSFGHDRKRDSDKTDTDWRTPPATDSFDDYLP

Parental  RRGDDSFGDKYRDRYDSDRYRDGY----RDGPRRDMDRYGGRDRYDDRGSRDYDRGYESRIGSGRRAFGS
          RRGD.SFGD.YRDR.DSDRY.DGY....R.GP..DMD.YG.RD.Y.DRGSRDYDRGY.SRIGSGRRAF.S
Retrocopy RRGDNSFGD*YRDRCDSDRYHDGYRHG*RYGPHWDMD*YGSRDGYVDRGSRDYDRGYDSRIGSGRRAFDS

Parental  GYRRDDDYRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQ
          G..RDDDYRGG...YED.YDR.DD.SWSSRDDYSRDDY.RDDRG..QRPKLNLKPRSTPKEDDSSASTSQ
Retrocopy GCGRDDDYRGGRNGYEDLYDR*DDQSWSSRDDYSRDDYMRDDRGLSQRPKLNLKPRSTPKEDDSSASTSQ

Parental  SSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQERERSRTGSE
          .S..ASIFGGAK.VDTA.REREVEE.LQKE.EKLQR.LDEPKLER.PRERHPSW.SEET.ERE.SRTGSE
Retrocopy CSQGASIFGGAKHVDTATREREVEEQLQKEHEKLQR*LDEPKLERQPRERHPSWQSEETREREQSRTGSE

Parental  SSQTGTSATSGRNARRR-ESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSSNPP
          SSQTGTSATSGRNA.RR.E.EKSLENETLNKEEDC.S.TSKPPKPD.PLKV.PAP.PKEN.WVK.SS.PP
Retrocopy SSQTGTSATSGRNA-RR<EREKSLENETLNKEEDCQSLTSKPPKPDKPLKVTPAPSPKENGWVK*SSKPP

Parental  ARSQSSDTEQQSPTSGG-GKVAPAQPSEEGPARKDENKVDGMNVPKGQTGTSSRGPGDGGNKDHWKESDR
          A.SQSSDTEQQSPT.GG.GKVAPAQPSE.GPARKDE..VDGMNVPKGQTG.SS.GPG.GGNKDHWKESDR
Retrocopy AQSQSSDTEQQSPTTGG<GKVAPAQPSE*GPARKDEKEVDGMNVPKGQTGNSSHGPGEGGNKDHWKESDR

Parental  KDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYAE
          KDGKKD.DSRSAPE.KKPEENPASKFSSA.K.AALS.DGEDENEG.D.AE
Retrocopy KDGKKDKDSRSAPESKKPEENPASKFSSARKCAALSIDGEDENEGDD*AE

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	42.80 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	92.18 RPM
SRP007412_cerebellum	0.00 RPM	45.72 RPM
SRP007412_heart	0.00 RPM	75.55 RPM
SRP007412_kidney	0.00 RPM	50.47 RPM
SRP007412_liver	0.00 RPM	43.46 RPM
SRP007412_testis	0.04 RPM	80.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2589 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2589 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2589 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4848
Gorilla gorilla	retro_ggor_3024
Pongo abelii	retro_pabe_3768

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012023	2 retrocopies	retro_amel_1107, retro_amel_559,
Canis familiaris	ENSCAFG00000007117	2 retrocopies	retro_cfam_1447, retro_cfam_936,
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310, retro_chof_366,
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589 , retro_mmul_731, retro_mmul_783,
Macaca mulatta	ENSMMUG00000006205	2 retrocopies	retro_mmul_2634, retro_mmul_619,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,