RetrogeneDB ID: retro_cjac_1552

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:40549563..40549908(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS6
• Ensembl ID: ENSCJAG00000019382
• Aliases: None
• Description: None

Sequence

>retro_cjac_1552
TGCCAGCCGCTGGGCTGGAGCAGCATAGTGGTGTTGAGCATGCCCTCTGGTGCCAGGTGTTTTGGAGTATGGGCCTTGCC
AACTGGAGAGAAGGTCATGCATGCCAGACAGGTTGATGATAATAAAAACTCCAGGAAAGTTCAGTTTATGGGTTGTCAGA
AATAAGTGAATGTAAACTTTGCCACTGATTTGATAACAGAGCCACCTAAGAGTGAAGTAGGGAGTTGGGTAATATTGTGT
AACTGGTTGGGGAGCTCTCGGCTATCCAAAAGTGTGTAAATATAGAAAAAAACCCCCAAAACTGGGATATGTGGTTATTG
TGGACTATAGGTCAAAAAACACCAT

Alignment

ORF - retro_cjac_1552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.69 %
• Parental protein coverage: 93.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CRLLCRSGAAARSLSLGARCFGVQISPTGEKITHTGQVYDEKDYRRLRFVGRQKEVNENFGIDLIAEQPV
          C..L..S.....S...GARCFGV...PTGEK..H..QV.D.K..R...F.G.QK.VN.NF..DLI.E.P.
Retrocopy CQPLGWSSIVVLSMPSGARCFGVWALPTGEKVMHARQVDDNKNSRKVQFMGCQK*VNVNFATDLITEPPK

Parental  SEVEARVISCD-GGGGALGHPKVYINLDKETK-TGTCGYCGLQFRQHH
          SEV...VI.C..G.G.ALG.PKV.....K..K.TG.CGYCGL....HH
Retrocopy SEVGSWVILCN>GWG-ALGYPKVCKYRKKPPK<TGICGYCGL*VKKHH

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	0.00 RPM	9.45 RPM
SRP051959_heart	0.00 RPM	19.73 RPM
SRP051959_kidney	0.00 RPM	16.88 RPM
SRP051959_liver	0.00 RPM	12.02 RPM
SRP051959_lung	0.00 RPM	6.39 RPM
SRP051959_lymph_node	0.00 RPM	6.60 RPM
SRP051959_skeletal_muscle	0.00 RPM	21.82 RPM
SRP051959_spleen	0.04 RPM	5.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1552 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1552 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1552 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2838
Pan troglodytes	retro_ptro_1924
Pongo abelii	retro_pabe_2350
Macaca mulatta	retro_mmul_1473

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010930	2 retrocopies	retro_amel_213, retro_amel_228,
Bos taurus	ENSBTAG00000009914	2 retrocopies	retro_btau_302, retro_btau_333,
Callithrix jacchus	ENSCJAG00000019382	1 retrocopy	retro_cjac_1552 ,
Equus caballus	ENSECAG00000021690	3 retrocopies	retro_ecab_701, retro_ecab_838, retro_ecab_917,
Homo sapiens	ENSG00000145494	1 retrocopy	retro_hsap_2838,
Latimeria chalumnae	ENSLACG00000004625	1 retrocopy	retro_lcha_95,
Loxodonta africana	ENSLAFG00000005708	1 retrocopy	retro_lafr_5,
Myotis lucifugus	ENSMLUG00000016888	1 retrocopy	retro_mluc_1750,
Macaca mulatta	ENSMMUG00000004447	1 retrocopy	retro_mmul_1473,
Monodelphis domestica	ENSMODG00000001425	1 retrocopy	retro_mdom_207,
Mus musculus	ENSMUSG00000021606	1 retrocopy	retro_mmus_3044,
Nomascus leucogenys	ENSNLEG00000011199	1 retrocopy	retro_nleu_1593,
Oryctolagus cuniculus	ENSOCUG00000004581	2 retrocopies	retro_ocun_1011, retro_ocun_1624,
Pongo abelii	ENSPPYG00000015323	1 retrocopy	retro_pabe_2350,
Pan troglodytes	ENSPTRG00000016706	1 retrocopy	retro_ptro_1924,
Rattus norvegicus	ENSRNOG00000023387	1 retrocopy	retro_rnor_1619,
Rattus norvegicus	ENSRNOG00000049394	1 retrocopy	retro_rnor_1618,
Sarcophilus harrisii	ENSSHAG00000017779	1 retrocopy	retro_shar_176,
Ictidomys tridecemlineatus	ENSSTOG00000003715	1 retrocopy	retro_itri_496,