RetrogeneDB ID: retro_mmul_1152

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:59487491..59488231(+)
• Located in intron of: ENSMMUG00000023448

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAMM50
• Ensembl ID: ENSMMUG00000015446
• Aliases: None
• Description: sorting and assembly machinery component 50 homolog [Source:RefSeq peptide;Acc:NP_001248655]

Sequence

>retro_mmul_1152
AGTCTTCCCATATGAAAGACCAGCCACATCATCAATTGAAAAAGCACGTGGTGAGACCTGGACTGCCACTTAAGAACAGC
ATCATTTGCTGTTTGAAAGTAAGGCAGACATTCACTTAAATCATCTCTTTCACATGCCATGGTCATCGATTTTCAGAATT
CTTTCATCTTACCAAGAAAATGTGTTTTGCTGAAAGTTAACCAGGAACTGACAGGCTACACTGCAAGGGATGTAAGCTTC
ATCAAAGAAGATTTTGAACTTCAGTTGAATAAACCACTCATATTTGATTCAGTTTTTTCAGCATTTCTCTGAGGTGGGAT
GTTGGCAACCATGGTGATAAACTGTGAGTCCTGCTGCTAGTTTTACCTTGGGGAACCAAAAAGTGTCCAGGGATTCAGCA
TGCACAGCACCGCAGCAGAGTGCAGGCGACCACCTAGGTGAAGCAGCACGCTAGGCCAGTGGCCTGCATCTGTATACCCC
AACACGTTTAAAGCCAAGCCAATGCAGTTTGGGAGAACTTTTCCAAACACTTTTTCTCAACACAGGAAACCTCTGCAACC
TCAACTATGGGGAGGGCCCCAAAGTGTATTCGTGAGCTGGCTGAATGCATCTGCCAGTTTTATGGCACCAGGATTGTCTT
AAGGCTTGGCAAGATGGCTCTGTTGGAACTTAATTACTAAATTCCTGTGGGAGTGCAGACAGGCAACAGGATATGTGATA
GCATCTAGTTTTGAACTGGT

Alignment

ORF - retro_mmul_1152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.24 %
• Parental protein coverage: 53.3 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SFPIWKTSHTVKWEGVWRELGCLSRTASFAVRKESGHSLKSSLSHAMVIDSRNSSILPRRGALLKVNQEL
          S.PI.KTSH.......W..L.C..RTASFAV.K...HSLKSSLSHAMVID..NS.ILPR...LLKVNQEL
Retrocopy SLPI*KTSHIIN*KSTW*DLDCHLRTASFAV*K*GRHSLKSSLSHAMVIDFQNSFILPRKCVLLKVNQEL

Parental  AGYTGGDVSFIKEDFELQLNKQLIFDSVFSASLWGGMLVPI-GDK-PSSIADRFYLGGPTSVRGFSMHSI
          .GYT..DVSFIKEDFELQLNK.LIFDSVFSA.L.GGML....GDK...S.A..F.LG.....R..S....
Retrocopy TGYTARDVSFIKEDFELQLNKPLIFDSVFSAFL*GGMLATM<GDK<TVSPAASFTLGNQKVSRD-SACTA

Parental  GPQSEGDYLGGEAYWAGGLHLYTPLPFRPGQGGFGELFRTHFFLNAGNLCNLNYGEG-PKAHIRKLAECI
          ..QS.GD.LG..A..A.GLHLYTP....P.Q...GELF.T..FLN.GNLCNLNYGEG.PK..IR.LAECI
Retrocopy PQQSAGDHLGEAAR*ASGLHLYTPTRLKPSQCSLGELFQT-LFLNTGNLCNLNYGEG>PKC-IRELAECI

Parental  RWSYGAGIVLRLGNIARLELNYCIPMGVQTGDRICDGVQFGAG
          ...YG..IVLRLG..A.LELNY.IP.GVQTG.RICD...F..G
Retrocopy CQFYGTRIVLRLGKMALLELNY*IPVGVQTGNRICDSI*F*TG

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	30.25 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	36.89 RPM
SRP007412_cerebellum	0.00 RPM	29.32 RPM
SRP007412_heart	0.00 RPM	61.59 RPM
SRP007412_kidney	0.00 RPM	57.04 RPM
SRP007412_liver	0.00 RPM	83.80 RPM
SRP007412_testis	0.11 RPM	42.44 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1152 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1152 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4233
Pan troglodytes	retro_ptro_2876
Pongo abelii	retro_pabe_3404
Callithrix jacchus	retro_cjac_605

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015070	2 retrocopies	retro_cjac_2277, retro_cjac_605,
Homo sapiens	ENSG00000100347	1 retrocopy	retro_hsap_4233,
Macaca mulatta	ENSMMUG00000015446	1 retrocopy	retro_mmul_1152 ,
Nomascus leucogenys	ENSNLEG00000015693	1 retrocopy	retro_nleu_1035,
Pongo abelii	ENSPPYG00000011918	1 retrocopy	retro_pabe_3404,
Pan troglodytes	ENSPTRG00000014483	1 retrocopy	retro_ptro_2876,