RetrogeneDB ID: retro_mmul_373

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:54285170..54285464(+)
• Located in intron of: ENSMMUG00000012055

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSMMUG00000005240
• Aliases: None
• Description: small ubiquitin-related modifier 1 [Source:RefSeq peptide;Acc:NP_001182571]

Sequence

>retro_mmul_373
CAGGAGGCAAAACCTTCAACTGAGGACTTGGGAGATAAGAAGGAAGGTGAATATATTAAACTCAAAGTCATTGGACAGGA
TAGCAGTGAGATTCACTTCAAAGTGAAAATGACAACACATCTCAAGAAACTCTTAGAATCATATTGTCAAAGACAGGGCG
TTCCAATGAATTCAATCAGGTATCTCTTTGAGGGTCAGAGAATTGCTGATAATCATACTCCAAAAGAACTGGGAATGGAG
GAAGAAGATGTGATTGAAGTTTATCAGGAACAAACGGGGGGTCATTCAACAGTT

Alignment

ORF - retro_mmul_373 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.94 %
• Parental protein coverage: 97.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIAD
          QEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKL.ESYCQRQGVPMNS.R.LFEGQRIAD
Retrocopy QEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLLESYCQRQGVPMNSIRYLFEGQRIAD

Parental  NHTPKELGMEEEDVIEVYQEQTGGHSTV
          NHTPKELGMEEEDVIEVYQEQTGGHSTV
Retrocopy NHTPKELGMEEEDVIEVYQEQTGGHSTV

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	4.03 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	19.99 RPM
SRP007412_cerebellum	0.06 RPM	3.04 RPM
SRP007412_heart	0.12 RPM	1.59 RPM
SRP007412_kidney	0.00 RPM	4.23 RPM
SRP007412_liver	0.00 RPM	0.75 RPM
SRP007412_testis	0.08 RPM	1.28 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_373 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_373 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Choloepus hoffmanni	ENSCHOG00000009739	2 retrocopies	retro_chof_190, retro_chof_2068,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Loxodonta africana	ENSLAFG00000022855	5 retrocopies	retro_lafr_111, retro_lafr_1148, retro_lafr_189, retro_lafr_540, retro_lafr_951,
Microcebus murinus	ENSMICG00000008968	5 retrocopies	retro_mmur_1177, retro_mmur_1300, retro_mmur_1493, retro_mmur_1554, retro_mmur_1602,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Macaca mulatta	ENSMMUG00000005240	7 retrocopies	retro_mmul_1108, retro_mmul_2035, retro_mmul_2081, retro_mmul_313, retro_mmul_373 , retro_mmul_450, retro_mmul_855,
Macaca mulatta	ENSMMUG00000006760	3 retrocopies	retro_mmul_2131, retro_mmul_2215, retro_mmul_47,
Nomascus leucogenys	ENSNLEG00000006997	4 retrocopies	retro_nleu_277, retro_nleu_384, retro_nleu_855, retro_nleu_865,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Procavia capensis	ENSPCAG00000006870	1 retrocopy	retro_pcap_136,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,