RetrogeneDB ID: retro_mmul_1426

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:40368255..40369207(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTOV1
• Ensembl ID: ENSMMUG00000011618
• Aliases: None
• Description: prostate tumor overexpressed 1 [Source:HGNC Symbol;Acc:9632]

Sequence

>retro_mmul_1426
AACAAGCTGCTGACCTGGAGCGGCGTCCTCGAGTGACAGGAGAAGCGCAGACTCTACTCCGACTCCACTGTAAAGTTGAA
GCGCGCCCTGCTCTGCCAAGCCTACGTGAACCTGGAGACCAACCAGTGGCAGCTGAAGCTGATCATGCAGCTGATCCCGC
AGCAGCTGATGGCCACGTTGAGACCCCTGTTCCGCAACTCCCAGCTGGCACAGTTCCACTTCAGCAACAGAGACTGCGGC
TTGCTCAACAGGCTCTGCCGCATCATGAGCAACGGCTTCGCGGGCTGCATGCAGTTTCCCCACATCTCCCCCTGCAAGAT
GTGCGTGCTCATGTTCCTGTACTCTTCCAGGACGAAGATCTTCATGGGCTTCATCCCCTATGACCAGAGCGGCTTCGTCA
GCGCCATCCGGCAGGTCATCACTACCCACAAGCAGGCAGTGGGACCTGGTGGTGTCAACTCAGGCCCAGTCAACAAGAAG
TTCCTGGCGTGGAGCGGCGTCATGGAGTGGCAGGAACCCAGGCCTGATCCCAACAGTCGGTCCAAGAGGTGGCTGCGGTC
CCACGTCTACGTGAACCAGGGGAGATCCTGAGGACCGAGCAGTGGCCGAGGAAGCTGTACATGCAGCTCATTCCGCAGCA
GCTGCTGACCACCCTGGTGCTGCTGTTGCAGAACTAGCGCCTGGTGCACTTCCACTTCACCAAGGACCTGGAGACGCTGA
AGAGCCTGTGCCGGATCATGGACAATGGCTTCGCCGGGTGAGTGCACTTTTCCTACAAAGCGTCGTGGGAGATCCGTGTG
CTCATGCTCCTGTACTCCTCTGAGAAGAAAATCTTCATCGGCCTCATCCCCCAGGGCAACTTCCTCAATGGCATGCTGCA
AGTCATTGCCAACCAGCGCAGGTCCTGCAGTGGAACCTGGAACAGGAGCAGCAGCAGCAAGGAATGGGGGGT

Alignment

ORF - retro_mmul_1426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.28 %
• Parental protein coverage: 85.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKLLAWSGVLEWQEKRRPYSDSTAKLKRTLPCQAYVNQGENLETDQWPQKLIMQLIPQQLLTTLGPLFRN
          NKLL.WSGVLE.QEKRR.YSDST.KLKR.L.CQAYV....NLET.QW..KLIMQLIPQQL..TL.PLFRN
Retrocopy NKLLTWSGVLE*QEKRRLYSDSTVKLKRALLCQAYV----NLETNQWQLKLIMQLIPQQLMATLRPLFRN

Parental  SQLAQFHFTNRDCDSLKGLCRIMGNGFAGCMLFPHISPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVSAI
          SQLAQFHF.NRDC..L..LCRIM.NGFAGCM.FPHISPC...VLM.LYSS..KIFMG.IPYDQSGFVSAI
Retrocopy SQLAQFHFSNRDCGLLNRLCRIMSNGFAGCMQFPHISPCKMCVLMFLYSSRTKIFMGFIPYDQSGFVSAI

Parental  RQVITTRKQAVGPGGVNSGPVQIVNNKFLAWSGVMEWQEPRPEPNSRSKRWLPSHVYVNQ-GEILRTEQW
          RQVITT.KQAVGPGGVNSGPV...N.KFLAWSGVMEWQEPRP.PNSRSKRWL.SHVYVNQ.GEILRTEQW
Retrocopy RQVITTHKQAVGPGGVNSGPV---NKKFLAWSGVMEWQEPRPDPNSRSKRWLRSHVYVNQ<GEILRTEQW

Parental  PRKLYMQLIPQQLLTTLVPLFRNSRLVQFHFTKDLETLKSLCRIMDNGFAGCVHFSYKASCEIRVLMLLY
          PRKLYMQLIPQQLLTTLV.L..N.RLV.FHFTKDLETLKSLCRIMDNGFAG.VHFSYKAS.EIRVLMLLY
Retrocopy PRKLYMQLIPQQLLTTLVLLLQN*RLVHFHFTKDLETLKSLCRIMDNGFAG*VHFSYKASWEIRVLMLLY

Parental  SSEKKIFIGLIPHDQGNFVNGIRRVIANQQ-QVLQRNLEQEQQQRGMGG
          SSEKKIFIGLIP..QGNF.NG...VIANQ..QVLQ.NLEQEQQQ.GMGG
Retrocopy SSEKKIFIGLIP--QGNFLNGMLQVIANQR<QVLQWNLEQEQQQQGMGG

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	40.79 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	102.57 RPM
SRP007412_cerebellum	0.00 RPM	36.94 RPM
SRP007412_heart	0.00 RPM	31.62 RPM
SRP007412_kidney	0.12 RPM	60.09 RPM
SRP007412_liver	0.04 RPM	91.64 RPM
SRP007412_testis	0.08 RPM	55.82 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1426 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1426 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1426 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2694
Pan troglodytes	retro_ptro_1818
Gorilla gorilla	retro_ggor_1877
Pongo abelii	retro_pabe_2288

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003495	1 retrocopy	retro_cfam_289,
Callithrix jacchus	ENSCJAG00000004105	1 retrocopy	retro_cjac_445,
Homo sapiens	ENSG00000104960	1 retrocopy	retro_hsap_2694,
Gorilla gorilla	ENSGGOG00000010182	1 retrocopy	retro_ggor_1877,
Macaca mulatta	ENSMMUG00000011618	1 retrocopy	retro_mmul_1426 ,
Nomascus leucogenys	ENSNLEG00000005374	1 retrocopy	retro_nleu_1191,
Pongo abelii	ENSPPYG00000010265	1 retrocopy	retro_pabe_2288,
Pan troglodytes	ENSPTRG00000011321	1 retrocopy	retro_ptro_1818,