RetrogeneDB ID: retro_cjac_636

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:171572555..171572972(-)
• Located in intron of: ENSCJAG00000019817

Retrocopy information

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

Parental gene information

• Parental gene symbol: DAZAP2
• Ensembl ID: ENSCJAG00000017661
• Aliases: None
• Description: DAZ associated protein 2 [Source:HGNC Symbol;Acc:2684]

Sequence

>retro_cjac_636
CCTCAGGCTCCACATTATACTGATGCTCCACCTACCTACCCAGAGCTCTACCGTCCAAGGTTTGTGCACCCAGGGGCTGC
CACCGTCCCCACCAAGTCAGTCACATTTCCTGGAACCTCTCTGTATCTTCCCATGGCCCAGTTTGTGGCTGTTGGGTCTT
TAGGTTCCACAATCCCCATGGCTTATTATTCAGTCAGTCCCATCTATCCGCCTGGCTCTACAGTGCTGGTGGAAGGAAGG
TACAATGCAGGTGCCAAATTTGGAGCTGGGGCTACTGCTGGCAACATTCCTCCTCCACCTCCTGGATGCCCTCCCAATGC
TGCTCAGCTTGCAGTCATGCAGGGAGCCAATGTCCTCGTAACTCAGCAGAAAGGGAACGTCTTCATGGGTGGTTCAGATG
GTGGCTACACCATCTGG

Alignment

ORF - retro_cjac_636 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.77 %
• Parental protein coverage: 82.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQAPPYTDAPPAYSELYRPSFVHPGAATVPTMSAAFPGASLYLPMAQSVAVGPLGSTIPMAYYPVGPIYP
          PQAP.YTDAPP.Y.ELYRP.FVHPGAATVPT.S..FPG.SLYLPMAQ.VAVG.LGSTIPMAYY.V.PIYP
Retrocopy PQAPHYTDAPPTYPELYRPRFVHPGAATVPTKSVTFPGTSLYLPMAQFVAVGSLGSTIPMAYYSVSPIYP

Parental  PGSTVLVEGGYDAGARFGAGATAGNIPPPPPGCPPNAAQLAVMQGANVLVTQRKGNFFMGGSDGGYTIW
          PGSTVLVEG.Y.AGA.FGAGATAGNIPPPPPGCPPNAAQLAVMQGANVLVTQ.KGN.FMGGSDGGYTIW
Retrocopy PGSTVLVEGRYNAGAKFGAGATAGNIPPPPPGCPPNAAQLAVMQGANVLVTQQKGNVFMGGSDGGYTIW

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	0.35 RPM	21.34 RPM
SRP051959_heart	0.98 RPM	15.01 RPM
SRP051959_kidney	0.53 RPM	35.30 RPM
SRP051959_liver	0.17 RPM	21.01 RPM
SRP051959_lung	0.50 RPM	26.13 RPM
SRP051959_lymph_node	0.16 RPM	21.00 RPM
SRP051959_skeletal_muscle	0.22 RPM	7.95 RPM
SRP051959_spleen	0.32 RPM	24.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_636 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_636 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017661	2 retrocopies	retro_cjac_636 , retro_cjac_793,
Homo sapiens	ENSG00000183283	1 retrocopy	retro_hsap_2370,
Gorilla gorilla	ENSGGOG00000026861	1 retrocopy	retro_ggor_1800,
Myotis lucifugus	ENSMLUG00000009959	1 retrocopy	retro_mluc_351,
Macaca mulatta	ENSMMUG00000001884	1 retrocopy	retro_mmul_958,
Nomascus leucogenys	ENSNLEG00000017776	1 retrocopy	retro_nleu_360,
Otolemur garnettii	ENSOGAG00000007977	3 retrocopies	retro_ogar_2109, retro_ogar_2139, retro_ogar_3130,
Pongo abelii	ENSPPYG00000004524	1 retrocopy	retro_pabe_2140,