RetrogeneDB ID: retro_cjac_1836

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:124793184..124793682(+)
• Located in intron of: ENSCJAG00000011227

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ10B
• Ensembl ID: ENSCJAG00000003971
• Aliases: None
• Description: coenzyme Q10 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25819]

Sequence

>retro_cjac_1836
GCAGCTTAGACTGGTCAAATGGCCATGAGAAGGGTGGTTTCAGGATGCTGTCTGAAGTCGGCTACAGCCGGTGGACTATG
GGCTCTGGTGCAGGGGCCTGCGCAGAATGTCAGATGTTTAGCTTCCTGTGGCATACTGATGAGCAGAACTCTTCCACGAC
ATACCTCAATTTTGCCTAAGGAGATACGTGCAAAAACTTTCTTCCAAATAAATGTACCATTAATAAACAAAAGGAAAGAA
TATTCAGAAAGAAGAATTTTAGGATAGTTAATGCAGGAAATGTATGATGTAGTATCATGAATAGAGGATGACAAGCATTT
CATTACCTGGTACAAAAATTCAGATGTAATATCAAAGAGATCCAGATATTGTAAAACACGATTAGAAATTGGGTTTCCAT
CTCTGTTGGGGCTATATCTATCAGTAGTCACTTTGATGAAACCTCATTTGGGAAAGGCATCCTGTACTAATAGGAAACTT
CTCAATCATTTGGAGACT

Alignment

ORF - retro_cjac_1836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.69 %
• Parental protein coverage: 68.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AARTGQTALRRVVSGCRPKSATVAGTPAPAQAPVRNGRYLASCGILMSRTLPLHTSVLPKEICARSFFKI
          AA.TGQ.A.RRVVSGC..KSAT..G..A..Q.P..N.R.LASCGILMSRTLP.HTS.LPKEI.A..FF.I
Retrocopy AA*TGQMAMRRVVSGCCLKSATAGGLWALVQGPAQNVRCLASCGILMSRTLPRHTSILPKEIRAKTFFQI

Parental  AAPLINKRKEYSERRILGYSMQEMYDVVSGMEDYKHFVPWCKRSDVLSKRSGYCKTRLEIGFPPVLERYT
          ..PLINKRKEYSERRILG..MQEMYDVVS..ED.KHF..W.K.SDV.SKRS.YCKTRLEIGFP..L..Y.
Retrocopy NVPLINKRKEYSERRILG*LMQEMYDVVS*IEDDKHFITWYKNSDVISKRSRYCKTRLEIGFPSLLGLYL

Parental  SVVTLVKPHLVKASCTDGRLFKHLET
          SVVTL.KPHL.KASCT...L..HLET
Retrocopy SVVTLMKPHLGKASCTNRKLLNHLET

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	0.89 RPM	16.91 RPM
SRP051959_heart	0.49 RPM	16.70 RPM
SRP051959_kidney	0.51 RPM	25.94 RPM
SRP051959_liver	0.35 RPM	18.13 RPM
SRP051959_lung	0.99 RPM	16.61 RPM
SRP051959_lymph_node	0.78 RPM	16.64 RPM
SRP051959_skeletal_muscle	0.22 RPM	7.08 RPM
SRP051959_spleen	1.09 RPM	19.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1836 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1836 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2270
Pongo abelii	retro_pabe_2758

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004659	2 retrocopies	retro_btau_1595, retro_btau_1832,
Choloepus hoffmanni	ENSCHOG00000005807	1 retrocopy	retro_chof_1504,
Callithrix jacchus	ENSCJAG00000003971	1 retrocopy	retro_cjac_1836 ,
Dasypus novemcinctus	ENSDNOG00000003229	2 retrocopies	retro_dnov_1571, retro_dnov_2203,
Dipodomys ordii	ENSDORG00000004090	1 retrocopy	retro_dord_508,
Erinaceus europaeus	ENSEEUG00000001626	1 retrocopy	retro_eeur_401,
Felis catus	ENSFCAG00000022385	1 retrocopy	retro_fcat_1487,
Homo sapiens	ENSG00000115520	1 retrocopy	retro_hsap_3349,
Gorilla gorilla	ENSGGOG00000023373	2 retrocopies	retro_ggor_2270, retro_ggor_569,
Myotis lucifugus	ENSMLUG00000000865	1 retrocopy	retro_mluc_1236,
Macaca mulatta	ENSMMUG00000010488	1 retrocopy	retro_mmul_2434,
Monodelphis domestica	ENSMODG00000012281	1 retrocopy	retro_mdom_600,
Mus musculus	ENSMUSG00000025981	1 retrocopy	retro_mmus_3224,
Nomascus leucogenys	ENSNLEG00000006871	1 retrocopy	retro_nleu_1172,
Ochotona princeps	ENSOPRG00000010091	3 retrocopies	retro_opri_1020, retro_opri_173, retro_opri_664,
Pongo abelii	ENSPPYG00000013045	2 retrocopies	retro_pabe_2758, retro_pabe_576,
Pan troglodytes	ENSPTRG00000012772	1 retrocopy	retro_ptro_2137,
Rattus norvegicus	ENSRNOG00000014456	1 retrocopy	retro_rnor_1620,
Tarsius syrichta	ENSTSYG00000012642	2 retrocopies	retro_tsyr_1213, retro_tsyr_1666,