RetrogeneDB ID: retro_mmul_2574

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:45544190..45544814(-)
• Located in intron of: None

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_2574
CACCTAGCAGGACCACACCGCTATTTAGCAACCTATACAAACAAAAACGGCAGCCTTACCAATTTGAGAATTTATTCACA
TGGATTGGAGTTACTGGACCTTCAGAGTTACGATGGTGACGCACAAGGCAAAGAAGAGATCAACAGTCTTTTGAACAAAG
GAGAAGAAAGAATGAAAGAACTGAGTCAAGACAGTACTTGGTGGATGAGGCGATTACCACCTATAGTTCCAGGAGGAACC
ACCGACAGATATTGGCCCACAGCAGATGGACTCCTGGTTGAATACAATGTAGATGAAGTGGTATATGATGAAGATTCACC
TTATCAGAGCATTAAAATTCTACACTCGAAGCAATTTGGAAATATTCTCATCCTTAGTGGGAATGTCAACTTGGCAGAGA
GTGATTTGACATATACCTGGGCCATCGTGGGCAGTGGCAAAGATTACACTGGCAAAGATGTACTCATTCTGGGAGGCTGA
GATGGGGGCATATTGTGTGAAATAGTCGAACTAAAACTAAAGATGGTCACTATGATAGAGATTGATGAAATGGTGATTGA
TGGATGTAAGAGATATATGCGGACTTGTGGTGATGTCTTAGATAATCTTAAAGGAGACTGCTAT

Alignment

ORF - retro_mmul_2574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.86 %
• Parental protein coverage: 59.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HTWQDHGYLATYTNKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEEIDSILNKVEERMKELSQDSTGRVK
          H....H.YLATYTNKNGS..NLRIY.HGL.LLDLQSYDGDAQGKEEI.S.LNK.EERMKELSQDST....
Retrocopy HLAGPHRYLATYTNKNGSLTNLRIYSHGLELLDLQSYDGDAQGKEEINSLLNKGEERMKELSQDSTWWMR

Parental  RLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTR
          RLPPIV.GG..DRYWPTADG.LVEY..DEVVYDEDSPYQ.IKILHSKQFGNILILSG.VNLAESDL.YT.
Retrocopy RLPPIVPGGTTDRYWPTADGLLVEYNVDEVVYDEDSPYQSIKILHSKQFGNILILSGNVNLAESDLTYTW

Parental  AIMGSGKEDYTGKDVLILGGGDGGILYEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCY
          AI.GSGK.DYTGKDVLILGG.DGGIL.EIV.LK.KMVTM.EID.MVIDGCK.YMR.TCGDVLDNLKGDCY
Retrocopy AIVGSGK-DYTGKDVLILGG*DGGILCEIVELKLKMVTMIEIDEMVIDGCKRYMR-TCGDVLDNLKGDCY

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	52.33 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	34.75 RPM
SRP007412_cerebellum	0.00 RPM	54.76 RPM
SRP007412_heart	0.00 RPM	71.66 RPM
SRP007412_kidney	0.00 RPM	88.61 RPM
SRP007412_liver	0.00 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_2574 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2574 has 0 orthologous retrocopies within eutheria group .

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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,