RetrogeneDB ID: retro_mmul_1431

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:47573815..47574249(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRR3
• Ensembl ID: ENSMMUG00000013893
• Aliases: None
• Description: proline-rich protein 3 [Source:RefSeq peptide;Acc:NP_001244515]

Sequence

>retro_mmul_1431
CCAAATCCCCCTGCAACCTTTGCTGCCGCCATAATGCCGAAACAAAAGAAGCAGAATCAGCAGCAGCCCCCGCCACAGCA
GCAGCCCCCACTGCCCAAGTAGGAAGAGACTGGAGATGAGGAGGATGGGAGTCCTATCGGACCACCCCACCTTCTGAGCC
TCCCGCCATGGTCAGTCTAAAACCTGATGACCCTAAGTCAGCTCCTCACAGAGGTCCTCCAGGAGCAAAGGGACCGCTGA
TTCCACCGCTGCTGAGCCTCCCACCTCCCCCTCAGGGTAGAGGCCCAAGGCCAGGAGGCTTTGGCCCCAGGCCTAGCCCA
TATGGTTGTGGTTGGTGGGGAGTCAATGCTGAACCTCCTTTTCCAGGGCCAGGCCATAGGGGTCCCGCCAGGTGAAGGCT
TCACAAAGAACAGAGAAACCCTCCAAGCCTCCAA

Alignment

ORF - retro_mmul_1431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.34 %
• Parental protein coverage: 57.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PNPAAAIAAATMPKRKKQNQHQPPTQQQPPLPEREETGDEEDGSPIGPPSLLG-PPPMANGKPGDPKSAL
          PNP.A..AAA.MPK.KKQNQ.QPP.QQQPPLP..EETGDEEDGSPIGPP.LL..PP.M...KP.DPKSA.
Retrocopy PNPPATFAAAIMPKQKKQNQQQPPPQQQPPLPK*EETGDEEDGSPIGPPHLLS<PPAMVSLKPDDPKSAP

Parental  HRGPPGSRGPLIPPLLSLPPPPWGRGPIRRGLGPRSSPYGRGWWGVNVEPPFPGPGHGGPTRGSFHKEQR
          HRGPPG..GPLIPPLLSLPPPP.GRGP...G.GPR.SPYG.GWWGVN.EPPFPGPGH.GP.R...HKEQR
Retrocopy HRGPPGAKGPLIPPLLSLPPPPQGRGPRPGGFGPRPSPYGCGWWGVNAEPPFPGPGHRGPAR*RLHKEQR

Parental  NPRRLK
          NP..L.
Retrocopy NPPSLQ

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	16.25 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	18.56 RPM
SRP007412_cerebellum	0.00 RPM	16.47 RPM
SRP007412_heart	0.00 RPM	3.77 RPM
SRP007412_kidney	0.00 RPM	7.98 RPM
SRP007412_liver	0.00 RPM	5.15 RPM
SRP007412_testis	0.00 RPM	5.73 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1431 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1431 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1431 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2753

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022770	1 retrocopy	retro_cpor_775,
Felis catus	ENSFCAG00000025918	2 retrocopies	retro_fcat_1094, retro_fcat_1698,
Gorilla gorilla	ENSGGOG00000014604	1 retrocopy	retro_ggor_1915,
Myotis lucifugus	ENSMLUG00000008758	1 retrocopy	retro_mluc_1567,
Macaca mulatta	ENSMMUG00000013893	1 retrocopy	retro_mmul_1431 ,
Nomascus leucogenys	ENSNLEG00000005104	1 retrocopy	retro_nleu_1548,
Otolemur garnettii	ENSOGAG00000004430	2 retrocopies	retro_ogar_1030, retro_ogar_1324,
Pongo abelii	ENSPPYG00000016409	1 retrocopy	retro_pabe_2279,
Pan troglodytes	ENSPTRG00000017929	1 retrocopy	retro_ptro_1861,
Sorex araneus	ENSSARG00000002747	2 retrocopies	retro_sara_143, retro_sara_9,
Ictidomys tridecemlineatus	ENSSTOG00000011829	1 retrocopy	retro_itri_126,
Tarsius syrichta	ENSTSYG00000000166	2 retrocopies	retro_tsyr_308, retro_tsyr_841,