RetrogeneDB ID: retro_cjac_2098

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:18973228..18973510(-)
• Located in intron of: ENSCJAG00000000768

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXYD6
• Ensembl ID: ENSCJAG00000013044
• Aliases: None
• Description: FXYD domain containing ion transport regulator 6 [Source:HGNC Symbol;Acc:4030]

Sequence

>retro_cjac_2098
ATGGAGGTGGTGCTGATCTTTCTATGCAGCCTGCTGGCCCTCATTGTCCTGGCCAGTGCAGCTGAGAAGGAGAAGGAAAT
TGATTCTTTTTATTATGACTACCAGACCCTGAGGATTGGGGACTGGTATGTGCTGTGGTCCTATTCTGTTTGGACCCTCC
TTATCCTAGGTTGCAGGTGCAAGTGCAGTTTCAATCAGAAGCCCAGGACCTCAGGAGAGGAGGAAGCCCTGGCAGAGAAC
CTCATCACTGCAAATGCAACAGAGCTCTAGAAAGTAGAGAAC

Alignment

ORF - retro_cjac_2098 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MELVLVFLCSLLAPTVLASAAEKEKEIDPFHYDYQTLRIG-GLVFAVVLFSVG-ILLILSRRCKCSFNQK
          ME.VL.FLCSLLA..VLASAAEKEKEID.F.YDYQTLRIG.GLV.AVVLF.....L....R.CKCSFNQK
Retrocopy MEVVLIFLCSLLALIVLASAAEKEKEIDSFYYDYQTLRIG<GLVCAVVLFCLD>LLILGCR-CKCSFNQK

Parental  PRAPGDEEAQVENLITANATEPQKAEN
          PR..G.EEA..ENLITANATE..K.EN
Retrocopy PRTSGEEEALAENLITANATEL*KVEN

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	0.02 RPM	2.64 RPM
SRP051959_heart	0.21 RPM	3.16 RPM
SRP051959_kidney	0.02 RPM	0.35 RPM
SRP051959_liver	0.09 RPM	1.45 RPM
SRP051959_lung	0.07 RPM	1.04 RPM
SRP051959_lymph_node	0.09 RPM	1.94 RPM
SRP051959_skeletal_muscle	0.07 RPM	0.46 RPM
SRP051959_spleen	0.19 RPM	13.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2098 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2098 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2098 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013044	1 retrocopy	retro_cjac_2098 ,
Erinaceus europaeus	ENSEEUG00000011989	1 retrocopy	retro_eeur_382,
Homo sapiens	ENSG00000137726	2 retrocopies	retro_hsap_562, retro_hsap_662,
Gorilla gorilla	ENSGGOG00000006473	2 retrocopies	retro_ggor_507, retro_ggor_574,
Macaca mulatta	ENSMMUG00000007617	2 retrocopies	retro_mmul_2439, retro_mmul_2440,
Nomascus leucogenys	ENSNLEG00000007348	2 retrocopies	retro_nleu_1982, retro_nleu_2890,
Otolemur garnettii	ENSOGAG00000015394	2 retrocopies	retro_ogar_2451, retro_ogar_3061,
Pongo abelii	ENSPPYG00000003918	3 retrocopies	retro_pabe_583, retro_pabe_644, retro_pabe_648,
Pan troglodytes	ENSPTRG00000004329	3 retrocopies	retro_ptro_3127, retro_ptro_421, retro_ptro_481,