RetrogeneDB ID: retro_cjac_3405

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01178264.1:12539..12728(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000036789
• Aliases: None
• Description: None

Sequence

>retro_cjac_3405
AGGTGGGAGGATCACTTGAGGCCAGGAGTTCAAGACAAGCCTGAACAACATTTTGAGACCCTATCTATTCCTACCAAAAA
AATTAAAAAATAAAAAATTAGCTAGTCATGGTGGCACTTTCCTGTAGTCCTAGCTACTTGGGAAGCTGAGACAGAAGGAT
CACTTTAGCTCAGAAGGTCAAGGCTGCAG

Alignment

ORF - retro_cjac_3405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKENCLNPGDRDHPGQHGET---PTKK----KISWARWFTPVIPALWEAEVGGSPEPRRSRLQ
          R.E..L.PG..D.P.QH.ET...PTKK....KIS...W..PV..A.WEAE..GS...RRSRLQ
Retrocopy RWEDHLRPGVQDKPEQHFETLSIPTKKIKK*KIS*SWWHFPVVLATWEAETEGSL*LRRSRLQ

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	1.11 RPM
SRP051959_heart	0.00 RPM	0.63 RPM
SRP051959_kidney	0.00 RPM	0.73 RPM
SRP051959_liver	0.00 RPM	0.71 RPM
SRP051959_lung	0.00 RPM	0.85 RPM
SRP051959_lymph_node	0.00 RPM	0.87 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.39 RPM
SRP051959_spleen	0.00 RPM	0.78 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3405 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3405 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3405 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000036789	16 retrocopies	retro_cjac_3405 , retro_cjac_3412, retro_cjac_3413, retro_cjac_3442, retro_cjac_3458, retro_cjac_3465, retro_cjac_3492, retro_cjac_3508, retro_cjac_3520, retro_cjac_3542, retro_cjac_3611, retro_cjac_3625, retro_cjac_3676, retro_cjac_3745, retro_cjac_3767, retro_cjac_3806,