RetrogeneDB ID: retro_cjac_624

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:144845485..144845989(-)
• Located in intron of: ENSCJAG00000016471

Retrocopy information

• Ensembl ID: ENSCJAG00000033290
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WDR92
• Ensembl ID: ENSCJAG00000006498
• Aliases: None
• Description: calcineurin subunit B type 1 [Source:RefSeq peptide;Acc:NP_001257649]

Sequence

>retro_cjac_624
ATGGGAAACGAGGCCAGTTACCCGGCTGAGATGTGCTCCCACTTTGACAATGATGAAATCAAAAGGCTGGGCAGGAGCTT
TAAGAAGTTGGACTTGGACAAATCAGGCTCTCTGAGCGTGCAGGAGTTCATGTCCCTGCCGGAGCTGCGCCACAACCCGT
TGGTGCAGCGAGTGATCGACGTCTTCGACACCAACGGCAATGGAGAGGTGGACTTCAAGGAATTCATCCGGGGGATCTCC
CAGTTCAGCGTCAAGAGCAACGAGGAGCAGAAGCTGAGGTTTGCGTTCAGCATTTACGACATGGATAAAGATGGCTACAT
TTCCAACGGGGAGCTCTTCCAGGTGCTGAAGATGATAGTGGGTGACAACCTGAAGGACTGGCAGCTCCAGCAGCTGGTCG
ACAAAACCATCATCATCCTGGACAGGGATGGCGATGGGAAGATATCCTTTGAGGAATTCAGTGCTGTGGTCAGAGACCTC
GAGATCCACAAGAAGCTGGTCCTC

Alignment

ORF - retro_cjac_624 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 98.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEV
          MGNEASYP.EMCSHFD.DEIKRLG..FKKLDLD.SGSLSV.EFMSLPEL..NPLVQRVID.FDT.GNGEV
Retrocopy MGNEASYPAEMCSHFDNDEIKRLGRSFKKLDLDKSGSLSVQEFMSLPELRHNPLVQRVIDVFDTNGNGEV

Parental  DFKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINA
          DFKEFI.G.SQFSVK...EQKLRFAF.IYDMDKDGYISNGELFQVLKM.VG.NLKD.QLQQ.VDKTII..
Retrocopy DFKEFIRGISQFSVKSNEEQKLRFAFSIYDMDKDGYISNGELFQVLKMIVGDNLKDWQLQQLVDKTIIIL

Parental  DKDGDGRISFEEFCAVVGGLDIHKKMVV
          D.DGDG.ISFEEF.AVV..L.IHKK.V.
Retrocopy DRDGDGKISFEEFSAVVRDLEIHKKLVL

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	19.52 RPM
SRP051959_heart	0.04 RPM	18.79 RPM
SRP051959_kidney	0.00 RPM	18.99 RPM
SRP051959_liver	0.02 RPM	15.94 RPM
SRP051959_lung	0.02 RPM	24.03 RPM
SRP051959_lymph_node	0.00 RPM	23.04 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.94 RPM
SRP051959_spleen	0.00 RPM	26.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_624 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_624 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3
Pan troglodytes	retro_ptro_2909
Macaca mulatta	retro_mmul_1141
Oryctolagus cuniculus	retro_ocun_272
Bos taurus	retro_btau_1660
Sus scrofa	retro_sscr_86
Equus caballus	retro_ecab_651

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010619	1 retrocopy	retro_btau_1660,
Callithrix jacchus	ENSCJAG00000006498	1 retrocopy	retro_cjac_624 ,
Callithrix jacchus	ENSCJAG00000020761	1 retrocopy	retro_cjac_2396,
Dipodomys ordii	ENSDORG00000019760	1 retrocopy	retro_dord_404,
Equus caballus	ENSECAG00000009627	1 retrocopy	retro_ecab_651,
Felis catus	ENSFCAG00000028482	1 retrocopy	retro_fcat_1639,
Homo sapiens	ENSG00000221823	1 retrocopy	retro_hsap_3,
Loxodonta africana	ENSLAFG00000022682	1 retrocopy	retro_lafr_1014,
Macaca mulatta	ENSMMUG00000017460	1 retrocopy	retro_mmul_1141,
Mustela putorius furo	ENSMPUG00000006250	1 retrocopy	retro_mputfur_537,
Nomascus leucogenys	ENSNLEG00000026538	1 retrocopy	retro_nleu_1049,
Oryctolagus cuniculus	ENSOCUG00000027562	1 retrocopy	retro_ocun_272,
Otolemur garnettii	ENSOGAG00000034876	1 retrocopy	retro_ogar_1011,
Pan troglodytes	ENSPTRG00000041941	1 retrocopy	retro_ptro_2909,
Rattus norvegicus	ENSRNOG00000043210	1 retrocopy	retro_rnor_1932,
Sus scrofa	ENSSSCG00000022362	1 retrocopy	retro_sscr_86,
Ictidomys tridecemlineatus	ENSSTOG00000025985	1 retrocopy	retro_itri_1569,
Tarsius syrichta	ENSTSYG00000019531	2 retrocopies	retro_tsyr_326, retro_tsyr_41,
Tursiops truncatus	ENSTTRG00000021395	1 retrocopy	retro_ttru_382,
Vicugna pacos	ENSVPAG00000015522	1 retrocopy	retro_vpac_3,
Drosophila melanogaster	FBgn0015614	1 retrocopy	retro_dmel_53,