RetrogeneDB ID: retro_cjac_4064

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:52388688..52388922(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031713
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000006876
• Aliases: None
• Description: None

Sequence

>retro_cjac_4064
AAAGTGAAGACGCTGACCGGAAAGGAGATTAAGATTGACATTGAACCTACAGATAAGGTGGAGCGAATCAAGGAGCGTGT
GGAGGAGAAACAGGGAATCCCCCCACAACAGCAGAGGCTCATCTACAGTGGCAAACAGATGAATGATGAGAAGACAACAG
CTGATTACAAGATTTTAGGTGGTTCAGTCCTCCACCTCATGTTGGCTCTGAGAGGAGGAGGTGGTCTTAGGCAG

Alignment

ORF - retro_cjac_4064 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.67 %
• Parental protein coverage: 96.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLAL
          KVKTLTGKEI.IDIEPTDKVERIKERVEEK.GIPPQQQRLIYSGKQMNDEKT.ADYKILGGSVLHL.LAL
Retrocopy KVKTLTGKEIKIDIEPTDKVERIKERVEEKQGIPPQQQRLIYSGKQMNDEKTTADYKILGGSVLHLMLAL

Parental  RGGGGGLRQ
          R.GGGGLRQ
Retrocopy R-GGGGLRQ

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	10.74 RPM
SRP051959_heart	0.00 RPM	16.89 RPM
SRP051959_kidney	0.04 RPM	17.13 RPM
SRP051959_liver	0.00 RPM	16.70 RPM
SRP051959_lung	0.00 RPM	14.82 RPM
SRP051959_lymph_node	0.00 RPM	12.81 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.37 RPM
SRP051959_spleen	0.00 RPM	16.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4064 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4064 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038842	1 retrocopy	retro_btau_89,
Canis familiaris	ENSCAFG00000012097	1 retrocopy	retro_cfam_1789,
Choloepus hoffmanni	ENSCHOG00000001228	5 retrocopies	retro_chof_1012, retro_chof_1616, retro_chof_2696, retro_chof_613, retro_chof_788,
Callithrix jacchus	ENSCJAG00000006876	1 retrocopy	retro_cjac_4064 ,
Cavia porcellus	ENSCPOG00000010930	1 retrocopy	retro_cpor_371,
Erinaceus europaeus	ENSEEUG00000011640	2 retrocopies	retro_eeur_165, retro_eeur_43,
Echinops telfairi	ENSETEG00000018391	2 retrocopies	retro_etel_1118, retro_etel_1677,
Homo sapiens	ENSG00000129559	1 retrocopy	retro_hsap_180,
Gorilla gorilla	ENSGGOG00000016105	1 retrocopy	retro_ggor_261,
Macaca mulatta	ENSMMUG00000029409	1 retrocopy	retro_mmul_2236,
Monodelphis domestica	ENSMODG00000003254	1 retrocopy	retro_mdom_1681,
Vicugna pacos	ENSVPAG00000009104	4 retrocopies	retro_vpac_270, retro_vpac_316, retro_vpac_480, retro_vpac_558,