RetrogeneDB ID: retro_mmul_1428

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:42650763..42651850(+)
• 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_1428
GATCGATATGGCGGCCAGGATCGCTATGATGACCCAGGCAGCAGAGACTTTGATAGAGGCTATGATTCCCAGATAGGCAC
TGGCAGAAGAGCGTTTGGCAGTGGGTACCGCAGGGATAACCACTACAGAGGAGGCAGGGACCGCTCTGAAGACCGATGCA
ACAGATGCGATGATCGGTTGTGCAGCCCCAGAGATGATTACTCTCAGGATGATTATATGAGTGATGATAGAGGTCCCTCC
CAAAGACCCAAACTGAATCTAAAGCTTTGGAGTACTCCTAAGGAAGATGATTCCTCTGCTAGTACCTCCCAGTCCAGTCG
AGCTGCTTCTACCTTTGGAGGGGGAAAGCCCGTAGACACAGCTGCTAGAGAAAGAAGTAGAAGAACTGCTACAGAAGAAA
CAAGAGAAGTTACAGCGTCAACTGGATGAGCCATAACTAGAACGATGGCCTCGGGAGAGACACCCAAGCTGGTGAAGTGA
AGAAACTCAGGAACGGGAATGGTCGCGGACAGGAAGTGAGTCATCGCAGACTGGGACTTCCGCCACACCCAGCAGAAATG
CACGAAGGAGAGAGAGTGAGAAGTCTCTAGAAAACGCAACACTCAATAAGAAGGAAGATTGTCACTCTCCAACTTCTAAA
CCTCCCAAACCTGATCCTACCTGACCCAAAGGTAATGCCAGCCCCTCCACCAAAGGAGAATGCTTCGGTGAAGCAAAGTT
CTAACCCTCCTGCTCCATTTCAGAGCTCCGACACAGAGCAGCAATCCCCTACAAGTGGTGGGGGAAAGTAGCTCCAGCTC
AATAATCTGAGGAAGGACCAGCAAGGAAAGATGAAAGTAAAGTGGATGGGATGAATGTCCCAAAAGGCCAAACTGGGAAC
TCTAACTGTAGTCCAGGAAATGGAGGGAACAAAGACCACTGGAAGGAGTCAGATGGGAAAGATGGCAAAAAGGATCAAGA
CTCCAGATCTACACCTGAGCCAAAGAAACCGGAGGAAAATCCAGCTTCCAAGTTCAGTTCTGCAGCCAAGTATGCTGCTG
TCTCTGTTTCTGGTGAAGATGAAAACAAAGGAGAAGATTACGCCCAG

Alignment

ORF - retro_mmul_1428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.6 %
• Parental protein coverage: 59.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DRYGGRDRYDDRGSRDYDRGYESRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYDRRDDRSWSSRDDYSRD
          DRYGG.DRYDD.GSRD.DRGY.S.IG.GRRAFGSGYRRD..YRGG.DR.EDR..R.DDR..S.RDDYS.D
Retrocopy DRYGGQDRYDDPGSRDFDRGYDSQIGTGRRAFGSGYRRDNHYRGGRDRSEDRCNRCDDRLCSPRDDYSQD

Parental  DYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQSSRAASIFG-GAKPVDTAAREREVEERLQKEQEKLQ
          DY..DDRGP.QRPKLNLK..STPKEDDSSASTSQSSRAAS.FG.G..P..T...E.EVEE.LQK.QEKLQ
Retrocopy DYMSDDRGPSQRPKLNLKLWSTPKEDDSSASTSQSSRAASTFG>GESP*-TQLLEKEVEELLQKKQEKLQ

Parental  RQLDEPKLERRPRERHPSWRSEETQERERSRTGSESSQTGTSATSGRNARRRESEKSLENETLNKEEDCH
          RQLDEP.LER.PRERHPSW.SEETQERE.SRTGSESSQTGTSAT..RNARRRESEKSLEN.TLNK.EDCH
Retrocopy RQLDEP*LERWPRERHPSW*SEETQEREWSRTGSESSQTGTSATPSRNARRRESEKSLENATLNKKEDCH

Parental  SPTSKPPKPDQ-PLKVMPAPPP-KENAWVKRSSNPPARSQSSDTEQQSPTSGG-GKVAPAQPSEEGPARK
          SPTSKPPKPD..P.......PP.KENA.VK.SSNPPA..QSSDTEQQSPTSGG.GKVAPAQ.SEEGPARK
Retrocopy SPTSKPPKPDP>PDPKVMPAPPPKENASVKQSSNPPAPFQSSDTEQQSPTSGG<GKVAPAQ*SEEGPARK

Parental  DENKVDGMNVPKGQTGTSSRGPGDGGNKDHWKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAA
          DE.KVDGMNVPKGQTG.S...PG.GGNKDHWKESD.KDGKKDQDSRS.PEPKKPEENPASKFSSA.KYAA
Retrocopy DESKVDGMNVPKGQTGNSNCSPGNGGNKDHWKESDGKDGKKDQDSRSTPEPKKPEENPASKFSSAAKYAA

Parental  LSVDGEDENEGEDYAE
          .SV.GEDEN.GEDYA.
Retrocopy VSVSGEDENKGEDYAQ

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	1.62 RPM	80.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1428 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1428 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1882
Pongo abelii	retro_pabe_2283

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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,