RetrogeneDB ID: retro_cjac_2683

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:152299014..152299317(-)
• Located in intron of: None

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_2683
ACCACACCAAACAAGACACCTCCTGGTGCTGATCCTACTGGAGCAGTACAGGAAATTGGGTCACAAGCTGTTTGGTCACT
CTCATCTTGCAAACCAGGATTTGGAGTGGATCAGTTACGAGATGACAATCTAGAAGCTTATTAGCAATGAGATGGTTCCC
TTCATTTAGTGAACATCCAATTCAGAAGAAAAACAACAGTGAAGACATTATGTATTTATGCAGACTACAAATCTAATGAA
AGCTATACTCCAAGCAAGATCTCAGTCAGAGTAGGAAATAATTCTCACAACCTTCCAGAAATC

Alignment

ORF - retro_cjac_2683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.37 %
• Parental protein coverage: 55.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TPPGADPKQLERTGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVNIQFRRKTTVKT
          T.P...P.....TG.V.EIGSQAVWSLSSCKPGFGVDQLRDDNLE.Y.Q.DGS..HLVNIQFRRKTTVKT
Retrocopy TTPNKTPPGADPTGAVQEIGSQAVWSLSSCKPGFGVDQLRDDNLEAY*Q*DGSL-HLVNIQFRRKTTVKT

Parental  LCIYADYKSDESYTPSKISVRVGNNFHNLQEI
          LCIYADYKS.ESYTPSKISVRVGNN.HNL.EI
Retrocopy LCIYADYKSNESYTPSKISVRVGNNSHNLPEI

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	0.11 RPM	4.59 RPM
SRP051959_heart	0.07 RPM	3.24 RPM
SRP051959_kidney	0.16 RPM	5.75 RPM
SRP051959_liver	0.45 RPM	3.21 RPM
SRP051959_lung	0.13 RPM	5.11 RPM
SRP051959_lymph_node	0.11 RPM	5.46 RPM
SRP051959_skeletal_muscle	0.02 RPM	1.70 RPM
SRP051959_spleen	0.25 RPM	7.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2683 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2683 has 0 orthologous retrocopies within eutheria group .

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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,