RetrogeneDB ID: retro_mmul_2003

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:43155548..43156612(+)
• Located in intron of: ENSMMUG00000001224

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMS
• Ensembl ID: ENSMMUG00000020392
• Aliases: None
• Description: None

Sequence

>retro_mmul_2003
ATGCTTGGCGCCAAAGCTGGTGGTGAGACCATTCTAAAAAGCCTCCAGTCCATTTTCCAGAATCGGGGGATGGCGGAGTT
GGTGCACACCTGGAAGGACCATGGCTATTTAGCAACCTGCACAAACAAGAACAGCAGCTTTGCCAATTTGAGAATTTACC
TACATGGATTGTGTTGCTGGACCTTCAGAGTTACGATGGTGACGCGCAAGGCAAAGAAGAGATCAACAGTATTTTGAACA
AAGTAGAAGAAAGAATGAAAGAATTGAGTCAGGACTGTACTGGGCGGATAAAGCGATTACCACCCATAGTTGGAGGAGGA
GCCATCAACAGATATTGGCCCATTGCCGATGGGCGCCTGGTTGAATACGACATAGATTGAGGTGGTATATGATGAAGATT
CATCTTATCAAAATATAAAAATTCTACACTCGAAGCAGTTTGCAAATATTCTCATCCTGAGTGGGGATGTTAATTTACCA
GAGAGTGATTTGTTGTATACCTGGGCCATCATGGGCAGTGGCAAAGAAGATTACACTGGCAAAGATGTACTCATTCTGGG
AGACAAACGCGGGGGCATATTGTGTGAAATAGTCAAACTAAAACCAAAGATGGTCACTATGGTAAACTTGACCAAATGGT
GATCAATGGATGTAAGAAGTGTATGTGAAAAACGTGTGGCGATGTCTTAGACAATCTTAAAGGAGGCTGCTATCAGGTTC
TAATAGAAGACTGTATTCCGGTACTGAAGAAGTACGCCAAAGAAGGGAGATAATCTTATTACGTGATTAATGATTTGACA
GCTGTTCCAATCTCCATGTCTCCAGAAGAAGATTCCACATGGGAGTTTCCCAGACTGATTCTTGACCTCTCAATGAAAGT
ATTGAAACAGGATGGGAAGTACTTTACACAGGGGAAATGTGTCAATCTGACAGAAGCGCTGTCACTCTATGAAGAACAGC
TGGGGCGCCTGTATTGTCCTGTGGAATTCTCAAAGGAGATCGTCTGTGTCCCTTCGTACTTGGAATTGTGGGTATTTTAC
ACTCATTGAAAGAAAGCTAAACCT

Alignment

ORF - retro_mmul_2003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLGAKADGETILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGL-VLLDLQSYDGDA
          MLGAKA.GETILK.LQSIFQ..GMAE.VHTW.DHGYLAT.TNKN.SFANLRIY.HGL.VLLDLQSYDGDA
Retrocopy MLGAKAGGETILKSLQSIFQNRGMAELVHTWKDHGYLATCTNKNSSFANLRIYLHGL<VLLDLQSYDGDA

Parental  QGKEEIDSILNKVEERMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDID-EVVYDEDSPYQN
          QGKEEI.SILNKVEERMKELSQD.TGR.KRLPPIV.GGAI.RYWP.ADGRLVEYDID.EVVYDEDS.YQN
Retrocopy QGKEEINSILNKVEERMKELSQDCTGRIKRLPPIVGGGAINRYWPIADGRLVEYDID>EVVYDEDSSYQN

Parental  IKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILYEIVKLKPKMVTMV
          IKILHSKQF.NILILSGDVNL.ESDL.YT.AIMGSGKEDYTGKDVLILG...GGIL.EIVKLKPKMVTMV
Retrocopy IKILHSKQFANILILSGDVNLPESDLLYTWAIMGSGKEDYTGKDVLILGDKRGGILCEIVKLKPKMVTMV

Parental  -EIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSPEE
          ...DQMVI.GCKK.M.KTCGDVLDNLKG.CYQVLIEDCIPVLK.YAKEGR...YVINDLTAVPIS.SPEE
Retrocopy <KLDQMVINGCKKCM*KTCGDVLDNLKGGCYQVLIEDCIPVLKKYAKEGR*SYYVINDLTAVPISMSPEE

Parental  DSTWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGHLYCPVEFSKEIVCVPSYLELWVFY
          DSTWEF.RLILDLSMKVLKQDGKYFTQG.CVNLTEALSLYEEQLG.LYCPVEFSKEIVCVPSYLELWVFY
Retrocopy DSTWEFPRLILDLSMKVLKQDGKYFTQGKCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFY

Parental  TVWKKAKP
          T..KKAKP
Retrocopy TH*KKAKP

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	0.11 RPM	52.33 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	34.75 RPM
SRP007412_cerebellum	0.58 RPM	54.76 RPM
SRP007412_heart	0.24 RPM	71.66 RPM
SRP007412_kidney	0.12 RPM	88.61 RPM
SRP007412_liver	0.16 RPM	11.56 RPM
SRP007412_testis	0.00 RPM	12.48 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2003 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2003 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3168

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018382	1 retrocopy	retro_btau_1412,
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Cavia porcellus	ENSCPOG00000006176	2 retrocopies	retro_cpor_729, retro_cpor_889,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Homo sapiens	ENSG00000102172	5 retrocopies	retro_hsap_243, retro_hsap_3168, retro_hsap_3193, retro_hsap_3611, retro_hsap_4826,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta	ENSMMUG00000020392	2 retrocopies	retro_mmul_2003 , retro_mmul_2574,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Mus musculus	ENSMUSG00000071708	6 retrocopies	retro_mmus_2162, retro_mmus_2170, retro_mmus_2837, retro_mmus_3502, retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys	ENSNLEG00000009955	4 retrocopies	retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Pteropus vampyrus	ENSPVAG00000016785	1 retrocopy	retro_pvam_524,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Tupaia belangeri	ENSTBEG00000012109	3 retrocopies	retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,
Vicugna pacos	ENSVPAG00000007543	1 retrocopy	retro_vpac_50,