RetrogeneDB ID: retro_mmul_1746

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:3972481..3973378(+)
• Located in intron of: ENSMMUG00000014020

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4209
• Ensembl ID: ENSMMUG00000011476
• Aliases: None
• Description: sorting nexin-5 [Source:RefSeq peptide;Acc:NP_001244488]

Sequence

>retro_mmul_1746
CTTCAGATTCCAACTGCTCCTACGAAGCCTGACTTTGATGGTCCTCAAGAGACGATGCAGAAACTGGGAGAAGGTGAAGG
GTCTATGACCAAAGAAGAATTTGCCAAGATGATACAAGAACTGGAAGCTGAATATCTCGATGTTTTTAAGAAGACTGTGT
CCTCCCATGAAGTCTTTCTTCAATGGCTTTCATCTCACCCTGTTCTCAGTAAAGATCGCCACTTCCATGTTTTCCTAGAA
TATGATCAGGATCTAAGTGTTAGGTGGAAAAATACTAAAGGGATGTTTGGAGGCTTCTTCAAAAGTGTGGTGAAAAGTGC
TGAAGTCCTTTTTACTGGAGTTAAGGAGGTAGATGACTTCTTTGAGCAAGAGAAGAACTTCCTTATTAACTATTACAATA
GCATCAAAGATTCTTGTGTGAAAGCTGACAAAATGACCAGATCTCATAAAAATGTTACTGATGACTATATTCACACTGCA
GCCTGCTTACATAACCTGGCTTTAGAAGAGCCCACAGTCATCAAAAAGTACCCATTGAAGGTTGCTGAGCTATTTGAGAA
ACTTAGGAGAGTAGAGGGTTGAGTTTCATCAGATGAAGATTTGAAGCTAACAGAGCTCCTCTGATACTACACGCTCAACA
TCGAAGTTGCTAAGGATCTCTTATACAGACGCACCAAAGCCCTCATTGACTATGATAACTCAAACGAATCTCTGGATAAG
GTCCGGTTAAAGAGCAAAGACATCAAGTTGGCTGAGGCACACCAGCAGGAGTGCTGCCAGAAATTTGAACAACCTTCCAA
ATCTCCAAAAGAAGAACTGATAAATTTCAAACGGAAAGGAGTGGCAGCATTTAGAAAGAATCTACTTGAAACATCTGAAC
TGGAAATAAAACATGCC

Alignment

ORF - retro_mmul_1746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89. %
• Parental protein coverage: 74.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVSSHEVFLQRLSSHAILS
          L.IP.APTKPDFDGP.E.MQKLGEGEGSMTKEEFAKM.QELEAEYL.VFKKTVSSHEVFLQ.LSSH..LS
Retrocopy LQIPTAPTKPDFDGPQETMQKLGEGEGSMTKEEFAKMIQELEAEYLDVFKKTVSSHEVFLQWLSSHPVLS

Parental  KDRNFHVFLEYDQDLSVRRKNTKEMFGGFFKSVVKSADEVLFTGVKEVDDFFEQEKNFLINYYNRIKDSC
          KDR.FHVFLEYDQDLSVR.KNTK.MFGGFFKSVVKSA.EVLFTGVKEVDDFFEQEKNFLINYYN.IKDSC
Retrocopy KDRHFHVFLEYDQDLSVRWKNTKGMFGGFFKSVVKSA-EVLFTGVKEVDDFFEQEKNFLINYYNSIKDSC

Parental  VKADKMTRSHKNVADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLRKVEGRVSSDEDLKLTELLRY
          VKADKMTRSHKNV.DDYIHTAACLH.LALEEPTVIKKY.LKVAELFEKLR.VEG.VSSDEDLKLTELL.Y
Retrocopy VKADKMTRSHKNVTDDYIHTAACLHNLALEEPTVIKKYPLKVAELFEKLRRVEG*VSSDEDLKLTELL*Y

Parental  YMLNIEAAKDLLYRRTKALIDYENSNKALDKARLKSKDVKLAEAHQQECCQKFEQLSESAKEELINFKRK
          Y.LNIE.AKDLLYRRTKALIDY.NSN..LDK.RLKSKD.KLAEAHQQECCQKFEQ.S.S.KEELINFKRK
Retrocopy YTLNIEVAKDLLYRRTKALIDYDNSNESLDKVRLKSKDIKLAEAHQQECCQKFEQPSKSPKEELINFKRK

Parental  RVAAFRKNLIEMSELEIKHA
          .VAAFRKNL.E.SELEIKHA
Retrocopy GVAAFRKNLLETSELEIKHA

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	37.99 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	32.05 RPM
SRP007412_cerebellum	0.00 RPM	30.35 RPM
SRP007412_heart	0.00 RPM	32.56 RPM
SRP007412_kidney	0.00 RPM	70.77 RPM
SRP007412_liver	0.00 RPM	30.91 RPM
SRP007412_testis	0.00 RPM	15.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1746 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1746 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1746 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010128	2 retrocopies	retro_chof_1478, retro_chof_2166,
Callithrix jacchus	ENSCJAG00000004947	2 retrocopies	retro_cjac_2192, retro_cjac_3243,
Homo sapiens	ENSG00000089006	2 retrocopies	retro_hsap_1051, retro_hsap_2945,
Gorilla gorilla	ENSGGOG00000008953	1 retrocopy	retro_ggor_829,
Macropus eugenii	ENSMEUG00000009110	1 retrocopy	retro_meug_475,
Macaca mulatta	ENSMMUG00000011476	2 retrocopies	retro_mmul_1746 , retro_mmul_832,
Macaca mulatta	ENSMMUG00000019017	1 retrocopy	retro_mmul_1395,
Nomascus leucogenys	ENSNLEG00000009714	1 retrocopy	retro_nleu_2071,
Oryctolagus cuniculus	ENSOCUG00000017072	1 retrocopy	retro_ocun_1323,
Otolemur garnettii	ENSOGAG00000006157	1 retrocopy	retro_ogar_1203,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442, retro_pabe_877,
Pan troglodytes	ENSPTRG00000013278	2 retrocopies	retro_ptro_2052, retro_ptro_717,
Sus scrofa	ENSSSCG00000007088	1 retrocopy	retro_sscr_593,
Ictidomys tridecemlineatus	ENSSTOG00000015416	1 retrocopy	retro_itri_1176,
Tursiops truncatus	ENSTTRG00000016432	1 retrocopy	retro_ttru_410,