RetrogeneDB ID: retro_mmul_1153

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:63906417..63907080(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18006
• Ensembl ID: ENSMMUG00000023051
• Aliases: None
• Description: None

Sequence

>retro_mmul_1153
TCTATTTATATCAAAGGCTTCCCAACTGATGCAACTGTTGATGACATAAAAGAATGATTAGAAGATAGAGGTCAAGTACT
AACTATCCTGATGAGAAGAACATTGCATAAAGCATTTAAAGGATCAATGTTTGCTGTGTTTGGTAACAATGAATCTGCTA
AAAAGTTTGTAGAGACCCCTAGCCAGAAGTACAAAAACACAGTCTACTAATACTTTTCAAGAAATATTACTTTGCTGAAA
AAAGTGAAGAAAGGCAACAAAGTAATATGGAGGATAAATTAAGAGCAAAACAAGAGCAAGAAGGAAAATGAAAGCTAGAA
GATGCTGAAATGGAATCTCTTGAGAGAAAAGATTGGATGCTTGCTGAAATTTTTGGGTGACTTAGATGATCAGACCTGTA
GAGAAGGTTCACACATCCTTTTCTCAAATCATGGTGAACTAAAATGGATGACTTTGTCAGAGGTGCAAAAGAGGGAATAA
TTCGATTTAAAGAAAAAGTTGAGGAAGCGTTGGGAAAAGTCAAAGATGCAAATAATGGTAATCTACAATTAAGGAACAAA
GAAGTGACTTGGGAAGTACTAGAAGGACAGGTGGAAAAAGAAGCATTGAAAAATCATAAAAAGACCAACACTAATCCCCA
AACAAATGGAAGTCAAAAGGTCA

Alignment

ORF - retro_mmul_1153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 61.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPDQKYKET-DL
          S.YIKGFPTDAT.DDIKE.LED.GQVL.I.MRRTLHKAFKGS.F.VF...ESAKKFVETP.QKYK.T..L
Retrocopy SIYIKGFPTDATVDDIKE*LEDRGQVLTILMRRTLHKAFKGSMFAVFGNNESAKKFVETPSQKYKNT<SL

Parental  LILFKDDYFAKKNEERKQNKVEAKLRAKQEQEAKQKLEEDAEMKSLE-EKIGCLLKFSGDLDDQTCREDL
          LILFK..YFA.K.EER.Q...E.KLRAKQEQE.K.KL.EDAEM.SLE.EKIGCLLKF.GDLDDQTCRE..
Retrocopy LILFKKYYFAEKSEERQQSNMEDKLRAKQEQEGK*KL-EDAEMESLE>EKIGCLLKFLGDLDDQTCREGS

Parental  HILFSNHGEIKWI-DFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEDTEKN
          HILFSNHGE.KW..DFVRGAKEGII.FKEK..EALGK.KDANNGNLQLRNKEVTWEVLEG.VEKE...KN
Retrocopy HILFSNHGELKWM<DFVRGAKEGIIRFKEKVEEALGKVKDANNGNLQLRNKEVTWEVLEGQVEKE-ALKN

Parental  N-RRPTRIPKQMEVKRT
          ...RPT.IPKQMEVKR.
Retrocopy H>KRPTLIPKQMEVKRS

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	51.88 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	22.45 RPM
SRP007412_cerebellum	0.06 RPM	49.79 RPM
SRP007412_heart	0.00 RPM	32.68 RPM
SRP007412_kidney	0.00 RPM	37.09 RPM
SRP007412_liver	0.00 RPM	9.46 RPM
SRP007412_testis	0.00 RPM	33.66 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1153 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1153 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3408

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007763	5 retrocopies	retro_chof_1125, retro_chof_1292, retro_chof_1380, retro_chof_185, retro_chof_2593,
Dasypus novemcinctus	ENSDNOG00000013450	1 retrocopy	retro_dnov_2038,
Echinops telfairi	ENSETEG00000004614	1 retrocopy	retro_etel_2056,
Homo sapiens	ENSG00000138385	1 retrocopy	retro_hsap_448,
Gorilla gorilla	ENSGGOG00000023471	4 retrocopies	retro_ggor_2834, retro_ggor_2915, retro_ggor_433, retro_ggor_792,
Loxodonta africana	ENSLAFG00000000867	3 retrocopies	retro_lafr_698, retro_lafr_745, retro_lafr_982,
Macropus eugenii	ENSMEUG00000001650	1 retrocopy	retro_meug_1908,
Myotis lucifugus	ENSMLUG00000016316	1 retrocopy	retro_mluc_2493,
Macaca mulatta	ENSMMUG00000023051	2 retrocopies	retro_mmul_1153 , retro_mmul_529,
Monodelphis domestica	ENSMODG00000008227	1 retrocopy	retro_mdom_1080,
Nomascus leucogenys	ENSNLEG00000004958	3 retrocopies	retro_nleu_1039, retro_nleu_177, retro_nleu_3011,
Otolemur garnettii	ENSOGAG00000029768	1 retrocopy	retro_ogar_1642,
Pongo abelii	ENSPPYG00000012919	3 retrocopies	retro_pabe_3408, retro_pabe_3641, retro_pabe_424,
Pan troglodytes	ENSPTRG00000012620	1 retrocopy	retro_ptro_2509,
Rattus norvegicus	ENSRNOG00000007998	1 retrocopy	retro_rnor_405,
Tupaia belangeri	ENSTBEG00000009056	4 retrocopies	retro_tbel_1065, retro_tbel_1269, retro_tbel_3318, retro_tbel_4012,
Tursiops truncatus	ENSTTRG00000002152	2 retrocopies	retro_ttru_1926, retro_ttru_466,