RetrogeneDB ID: retro_cjac_3303

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:53485267..53485645(-)
• Located in intron of: ENSCJAG00000014762

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS25
• Ensembl ID: ENSCJAG00000017160
• Aliases: None
• Description: None

Sequence

>retro_cjac_3303
TTGCAGTACCCAGACCAGGGTGATGTAGTAGTGTTCAGGGACATGGTGAAGGTCATAACAGTGAATTATAACAAATATGA
GTTTCTGAGCGAAGGTGCCAGGAAATCTGCATTTTCCAACATACCTCAGATCCAATTTAAAAAACACTTGGATACAGATT
ATGATGTTTAAGAACATGATATCATTACCCTTCCTACAATTCTATTTATATTATGAAGAGCAGGTCCTGGTGGATACAGA
GATCAAGGTGAGTAAGGAGATCATGGAACACACCAAAAAAATCATTGGGAAGAATGAGGTCACGCTTAAGACCAAAAGGA
GCAGGAGAAAAAGCAGTTATCTCACCCAGCTCATTTGGCTTTCAAAGTATTTTTTCTG

Alignment

ORF - retro_cjac_3303 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.72 %
• Parental protein coverage: 71.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LQYLNQGNVV-FKDSVKVMTVNYNTRGELGEGARKFVFFNIPQIQYK-NPWVQIMMFKNMTPSPFLRFYL
          LQY..QG.VV.F.D.VKV.TVNYN....L.EGARK..F.NIPQIQ.K.N.W.QIMMFKNM...PFL.FYL
Retrocopy LQYPDQGDVVVFRDMVKVITVNYNKYEFLSEGARKSAFSNIPQIQFK>NTWIQIMMFKNMISLPFLQFYL

Parental  DSGEQVLVDVETKSNKEIMEHIRKILGKTEETLR-EEEE-EKKQLSHPANFGPRKYCL
          ...EQVLVD.E.K..KEIMEH..KI.GK.E.TL.....E.EKKQLSHPA........L
Retrocopy YYEEQVLVDTEIKVSKEIMEHTKKIIGKNEVTLK<DQKEQEKKQLSHPAHLAFKVFFL

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	0.24 RPM	6.79 RPM
SRP051959_heart	0.23 RPM	13.05 RPM
SRP051959_kidney	0.51 RPM	7.99 RPM
SRP051959_liver	0.19 RPM	12.87 RPM
SRP051959_lung	0.37 RPM	6.41 RPM
SRP051959_lymph_node	0.39 RPM	8.42 RPM
SRP051959_skeletal_muscle	0.24 RPM	13.32 RPM
SRP051959_spleen	0.34 RPM	9.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3303 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3303 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3303 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1127
Pan troglodytes	retro_ptro_678
Gorilla gorilla	retro_ggor_880
Pongo abelii	retro_pabe_932
Macaca mulatta	retro_mmul_874

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017160	1 retrocopy	retro_cjac_3303 ,
Homo sapiens	ENSG00000131368	1 retrocopy	retro_hsap_1127,
Gorilla gorilla	ENSGGOG00000011005	1 retrocopy	retro_ggor_880,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Macaca mulatta	ENSMMUG00000005157	2 retrocopies	retro_mmul_1946, retro_mmul_874,
Nomascus leucogenys	ENSNLEG00000005218	1 retrocopy	retro_nleu_184,
Pongo abelii	ENSPPYG00000013409	1 retrocopy	retro_pabe_932,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Pan troglodytes	ENSPTRG00000014658	1 retrocopy	retro_ptro_678,
Rattus norvegicus	ENSRNOG00000010912	1 retrocopy	retro_rnor_1184,
Ictidomys tridecemlineatus	ENSSTOG00000027997	1 retrocopy	retro_itri_984,