RetrogeneDB ID: retro_mmul_2455

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:69514339..69515274(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3225
• Ensembl ID: ENSMMUG00000013098
• Aliases: None
• Description: None

Sequence

>retro_mmul_2455
ATGGCCACCTTCGTAGAGCTCAGTACCAAAGCCAAGATGCCCATTGTGGGCCTGGGCACTTAGAAGTCTCCTCTCAGCAA
AATGAAAGAAGTGGTGAAGGTGGCCATTGCTGCAGGATATCGCCACATTGACTGTGCCTATGTCTAACAGAATGAACATG
AGGTGGGGGAAGTCATCCAAGAGAAGGCTGTGAAGCGGGAAGACCTCTTCATCATCAACAAGTTGTGGTCCACTTTCTTT
GAGAGACCCCTTGTGAGGAAGGCCTATGAGAAGACCCTCAAGGACCTGAAGCTTAGCTATCTGGATGTCTATCTTATTCA
CTAGCCACAGGGATTCAAGTCTGGGGATGACTTTTTCCCAAAAGATGACAAAGGTAATACGATCAGTGGAAAAGCAATGT
TCTTGGATGCCTGGGAGGCCGTGGAAGAGCTGATGGACGAGGGGCTGGCAAAAGCCTTTGGGGTCTCCAATTTCAACCAC
TTCCAGATAGAAAGGCTCTTGAACAAACCTGGACTGAAATATAAACCAGTGACTAATAGGCTGAGTGTCACCCATACCTC
ATGGAGGAGAAACTGATCCAGTACTGCCACTCCAAGGGCATCACCATTATGGCCTACAGCCCCTTAGGCTCTCCAGACAG
ATCTTGGGCCAAGCCAGAGGACCCTTCCCTGCTGGAGAACCTCAAGATTAAGGAGATTGCTGCAAAGCACAAAAAAACTG
CAGCCTGGGTTCTGATCTGTTTCCATATCCAGAGGAATGTGATTATGATCCCCAAGTCTGTGACACCAGCACGCATTGTT
GAGAACATTCAGGTCTTTGACTTTAAATTGAATGATGAGGAGATGGCAACCATACTCAGCTTCAACAGAAACTGGAAGGC
CTGTAACATGTTGCAATCCTCTCATTTGGAGGACTATCCCTTTGATGCAGAATAC

Alignment

ORF - retro_mmul_2455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVKVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEQAVKR
          MATFVELSTKAKMPIVGLGT.KSPL.K.KE.VKVAI.AGYRHIDCAYV.QNEHEVGE.IQEK....AVKR
Retrocopy MATFVELSTKAKMPIVGLGT*KSPLSKMKEVVKVAIAAGYRHIDCAYV*QNEHEVGEVIQEK----AVKR

Parental  EDLFIVSKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIHWPQGFKSGDDILPKDDKDNVIGGKATFLD
          EDLFI..KLW.TFFERPLVRKA.EKTLKDLKLSYLDVYLIH.PQGFKSGDD..PKDDK.N.I.GKA.FLD
Retrocopy EDLFIINKLWSTFFERPLVRKAYEKTLKDLKLSYLDVYLIH*PQGFKSGDDFFPKDDKGNTISGKAMFLD

Parental  AWEAMEELVDEGLVKALGISNFNHFQIERLLNKPGLKYKPVTNQV-ECHPYLTQEKLIQYCHSKGITVTA
          AWEA.EEL.DEGL.KA.G.SNFNHFQIERLLNKPGLKYKPVTN...ECHPYL..EKLIQYCHSKGIT..A
Retrocopy AWEAVEELMDEGLAKAFGVSNFNHFQIERLLNKPGLKYKPVTNRL<ECHPYLMEEKLIQYCHSKGITIMA

Parental  YSPLGSPDRPWAKPEDPSLLEDPKIKEIAAKHKKTAAQVLIRFHIQRNVIVIPKSVTPARIVENIQVFDF
          YSPLGSPDR.WAKPEDPSLLE..KIKEIAAKHKKTAA.VLI.FHIQRNVI.IPKSVTPARIVENIQVFDF
Retrocopy YSPLGSPDRSWAKPEDPSLLENLKIKEIAAKHKKTAAWVLICFHIQRNVIMIPKSVTPARIVENIQVFDF

Parental  KLSDEEMATILSFNRNWRACNMLQSSHLEDYPFDAEY
          KL.DEEMATILSFNRNW.ACNMLQSSHLEDYPFDAEY
Retrocopy KLNDEEMATILSFNRNWKACNMLQSSHLEDYPFDAEY

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	4.37 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.13 RPM
SRP007412_cerebellum	0.00 RPM	2.71 RPM
SRP007412_heart	0.00 RPM	29.62 RPM
SRP007412_kidney	0.00 RPM	8.57 RPM
SRP007412_liver	0.00 RPM	48.77 RPM
SRP007412_testis	0.00 RPM	6.56 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2455 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2455 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_581
Pan troglodytes	retro_ptro_428

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357, retro_mmul_2455 ,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,