RetrogeneDB ID: retro_cjac_3604

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01187817.1:22..414(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020022
• Aliases: None
• Description: None

Sequence

>retro_cjac_3604
CTAATTTTTGTAATTTTAGTAGAGATGGCATTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAAGTGATCC
ACCTGCCTTGGCCTCCCAAAATGATGGGATTATAGGCATGAGACACATACCCAAACCCTAGAGATATTTTTCTTCGTTTT
TTTTTTTTTTTTTTTTTCCTAAGATGGAGTCTCGCTCCATCACCAGGCTGGAGTGCAGTGGCATGATTAAAGCTCACTGC
AACTTCCACCTCCTGGGTTGAAGTGATCCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACAACAGGTGTGCACCGCCACAC
TCAGCTTATTTTTGTATTTTTAGTAGAGATGGAGACAATGTTGGCCAGGATGGTCTCGATCTCTTGGCTTCG

Alignment

ORF - retro_cjac_3604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.75 %
• Parental protein coverage: 88.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIFVFLVETGFLHVGQAGLKLFTSGDLPASASQSAVITGVSHCAWPSESNIILLFCFVLFFLRWSFTLVT
          LIFV.LVE..F.HVGQAGLKL.TS.D.PA.ASQ...I.G..H...P........F.F..FF........T
Retrocopy LIFVILVEMAFHHVGQAGLKLLTSSDPPALASQNDGIIGMRHIPKP*RYFSSFFFFF--FFPKMESRSIT

Parental  -QAGVQWCDLGSLQPPPPGFRQFSCLSLPSSWDYRHVPPCPAFCIFIEMEFYHVLQVGLELLTS
          .QAGVQW.D..SLQ.PPPG....SCLSL.SSWD.R..PP..A...........V.Q.GL.LL.S
Retrocopy <QAGVQWHD*SSLQLPPPGLK*SSCLSLLSSWDNRCAPPHSAYFCIFSRDGDNVGQDGLDLLAS

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	0.04 RPM	0.93 RPM
SRP051959_heart	0.02 RPM	1.19 RPM
SRP051959_kidney	0.02 RPM	1.18 RPM
SRP051959_liver	0.04 RPM	0.71 RPM
SRP051959_lung	0.03 RPM	0.67 RPM
SRP051959_lymph_node	0.00 RPM	1.10 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.44 RPM
SRP051959_spleen	0.11 RPM	0.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3604 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3604 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020022	17 retrocopies	retro_cjac_3346, retro_cjac_3351, retro_cjac_3366, retro_cjac_3378, retro_cjac_3408, retro_cjac_3432, retro_cjac_3434, retro_cjac_3453, retro_cjac_3467, retro_cjac_3585, retro_cjac_3604 , retro_cjac_3610, retro_cjac_3671, retro_cjac_3680, retro_cjac_3757, retro_cjac_3770, retro_cjac_3775,