RetrogeneDB ID: retro_cjac_2999

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:87838714..87839267(-)
• Located in intron of: ENSCJAG00000021597

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANAPC10
• Ensembl ID: ENSCJAG00000002663
• Aliases: None
• Description: anaphase promoting complex subunit 10 [Source:HGNC Symbol;Acc:24077]

Sequence

>retro_cjac_2999
ATGATTTCACCAAACAAGACATTCCTGGGGCTGATCCTAAGCAGTTGGAAAGAACTGGAACAGTACGGGAAACTGGGTCA
CTAGCTATTTGGTTTCTCTCATCTTGCAAACTAGGATTTAGAGTGGATCAGTTACGAGTTGACAATCTAGGAACTTACTG
GCAATCAGATGGCTCCCAACCTCATTTAGTGATTATCCAATTCAGAAGAAAAACAACAGTGGAGATATTATGTATTTATG
CAAGCTACAAATCTGGTGAAAGCTATACTCCAAGCAAGATCTCAGCCAGTGTAGGAAATAATTTTCAGAACCTTCAAGAA
ATTTGGCAACTTAAATTGGTAGAACCAAGTGGCTGAATTCACATTCTCTTAACTGATAATCAAAGGACACAAACTCACAC
ATTCATGATACAGATTGCTGTTCTAGCCAGTCATCAAAGTGGAAGAGACACCGGTATGAGAAAAGTTAAAATATACACAC
TGGTAGAAGAGAGCTCCATTGTAAGTTTCCTAGATATACAACTAAAGATTTCATGATGTATCATTCAATTAAG

Alignment

ORF - retro_cjac_2999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTTPNKT-PPGADPKQLERTGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVNIQFR
          M..PNKT..PGADPKQLERTGTVRE.GS.A.W.LSSCK.GF.VDQLR.DNL.TYWQSDGSQPHLV.IQFR
Retrocopy MISPNKT<IPGADPKQLERTGTVRETGSLAIWFLSSCKLGFRVDQLRVDNLGTYWQSDGSQPHLVIIQFR

Parental  RKTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQEIRQLELVEPSGWIHVPLTDNHKKPTRTFMIQI
          RKTTV..LCIYA.YKS.ESYTPSKIS..VGNNF.NLQEI.QL.LVEPSG.IH..LTDN....T.TFMIQI
Retrocopy RKTTVEILCIYASYKSGESYTPSKISASVGNNFQNLQEIWQLKLVEPSG*IHILLTDNQRTQTHTFMIQI

Parental  AVLANHQNGRDTHMRQIKIYTPVEESSI-GKFPRCTTIDFMMYRSIR
          AVLA.HQ.GRDT.MR..KIYT.VEESSI..KFPR.TT.DFMMY.SI.
Retrocopy AVLASHQSGRDTGMRKVKIYTLVEESSI<CKFPRYTTKDFMMYHSIK

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
SRP051959_colon	0.22 RPM	4.59 RPM
SRP051959_heart	0.28 RPM	3.24 RPM
SRP051959_kidney	0.42 RPM	5.75 RPM
SRP051959_liver	0.17 RPM	3.21 RPM
SRP051959_lung	0.33 RPM	5.11 RPM
SRP051959_lymph_node	0.18 RPM	5.46 RPM
SRP051959_skeletal_muscle	0.46 RPM	1.70 RPM
SRP051959_spleen	0.36 RPM	7.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2999 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2999 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
Macaca mulatta	retro_mmul_374

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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,