RetrogeneDB ID: retro_mmul_374

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:55080245..55080800(+)
• Located in intron of: ENSMMUG00000014327

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANAPC10
• Ensembl ID: ENSMMUG00000004432
• Aliases: None
• Description: None

Sequence

>retro_mmul_374
CTGACCACACCAAACAAGACATCTCCTGGTGCTGACCCTAAGCAGTTGGAAAGGACTAGAACAGTACGGGACATTGGGTC
ACAGGCTTTTTGGTCACTCTCATCTTGCAAACCAGGATTTGGAGTAGATCAGTTACGAGATGACAATCTAGAATCTTATT
GGCAATCAGATGGTTCCCAGCCTTATTTAGTGAACATCCAATTCAGAAGAAAAACAACAGTTAAGACATTATGTATTTAT
GCAGACTACAAATCTGATGAAAGCTATACTCCAAGCAAGATCTCAGCCAAAGTAGGAAATAATTTTCACAACCTTCAAGA
AATTCGGCAACTTGAATTGGTGGAACCAAGTGACTGGATTCACATTCCCTTAACTGATAATCATAAGAAGCCAACTCGCG
CATTCATGATACAGATTGCTGTTCTAGCCAGTCATCAAAATGGAAGAGACACCCATGTGAGACAAATTAAAATATACACA
CCGGTAGAAGAGAGCGCCATTGGTAAATTTCCTAGATATACAACTATAGAGTTCATGATGTGTTGTTCAATAAGA

Alignment

ORF - retro_mmul_374 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTPNKTPPGADPKQLERTGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVNIQFRR
          .TTPNKT.PGADPKQLERT.TVR.IGSQA.WSLSSCKPGFGVDQLRDDNLE.YWQSDGSQP.LVNIQFRR
Retrocopy LTTPNKTSPGADPKQLERTRTVRDIGSQAFWSLSSCKPGFGVDQLRDDNLESYWQSDGSQPYLVNIQFRR

Parental  KTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQEIRQLELVEPSGWIHVPLTDNHKKPTRTFMIQIA
          KTTVKTLCIYADYKSDESYTPSKIS..VGNNFHNLQEIRQLELVEPS.WIH.PLTDNHKKPTR.FMIQIA
Retrocopy KTTVKTLCIYADYKSDESYTPSKISAKVGNNFHNLQEIRQLELVEPSDWIHIPLTDNHKKPTRAFMIQIA

Parental  VLANHQNGRDTHMRQIKIYTPVEESSIGKFPRCTTIDFMMYRSIR
          VLA.HQNGRDTH.RQIKIYTPVEES.IGKFPR.TTI.FMM..SIR
Retrocopy VLASHQNGRDTHVRQIKIYTPVEESAIGKFPRYTTIEFMMCCSIR

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	4.37 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.22 RPM
SRP007412_cerebellum	0.45 RPM	3.36 RPM
SRP007412_heart	0.00 RPM	3.42 RPM
SRP007412_kidney	0.23 RPM	4.23 RPM
SRP007412_liver	0.08 RPM	1.46 RPM
SRP007412_testis	0.08 RPM	8.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_374 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_374 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_374 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_152
Pan troglodytes	retro_ptro_149
Gorilla gorilla	retro_ggor_241
Pongo abelii	retro_pabe_468
Callithrix jacchus	retro_cjac_2999

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002663	2 retrocopies	retro_cjac_2683, retro_cjac_2999,
Dipodomys ordii	ENSDORG00000016690	1 retrocopy	retro_dord_202,
Homo sapiens	ENSG00000164162	1 retrocopy	retro_hsap_152,
Gorilla gorilla	ENSGGOG00000025091	1 retrocopy	retro_ggor_241,
Myotis lucifugus	ENSMLUG00000008607	1 retrocopy	retro_mluc_1679,
Macaca mulatta	ENSMMUG00000004432	1 retrocopy	retro_mmul_374 ,
Mus musculus	ENSMUSG00000036977	1 retrocopy	retro_mmus_1511,
Nomascus leucogenys	ENSNLEG00000005453	1 retrocopy	retro_nleu_1498,
Otolemur garnettii	ENSOGAG00000006902	2 retrocopies	retro_ogar_1649, retro_ogar_2510,
Pongo abelii	ENSPPYG00000015096	1 retrocopy	retro_pabe_468,
Pan troglodytes	ENSPTRG00000016480	1 retrocopy	retro_ptro_149,
Pteropus vampyrus	ENSPVAG00000013169	2 retrocopies	retro_pvam_1245, retro_pvam_1450,