RetrogeneDB ID: retro_cjac_3378

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01176992.1:11812..12267(+)
• 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_3378
TTAATTTCTGTGTAGGTAGTAGAGATGAGGTTTCACCACATTGGCCAGGCTGCTCTCAGACTCCTGTCCTCAAATGATCC
ACCTGCCCTGGCCTCCCAAAATTCAGGGCTTACAGGTGTGAGCCACCCGCATTTGGCCAGTGATTGACTTTCATTTATTT
TATATATTTATTGATTTATTTTTTGAGATGGAGTTTCACTCTCATTACCCAGGCTGGAGTGCAATAGTGCGATCTTGGCT
CACGACAACCTCCGCCTCCTGGGTTCCAACGATTCTTCTGCCTCAGCCTCCTGAGTAGCTGGGATAACAGTTACGTGCCA
TCGTGCCCAGCTAAGTTTGCATTTTTAGTAGAGACAAGAGTTTTTAATGTTGGTCAGGCTGGTCTTGAACTCCTGACCTT
AGGTGATCTGCCTGCCTCGACCTCCCAAAGTGCTGAGACTACAGGTGTGAGCCAC

Alignment

ORF - retro_cjac_3378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIFVFLVETGFLHVGQAGLKLFTSGDLPASASQSAVITGVSHCAWPSESNIILLFCF-VLFFLRWSFTLV
          LI.V..VE..F.H.GQA.L.L..S.D.PA.ASQ....TGVSH....S......L.......FLRWSFTL.
Retrocopy LISV*VVEMRFHHIGQAALRLLSSNDPPALASQNSGLTGVSHPHLASD*LSFILYIY<LIYFLRWSFTLI

Parental  TQAGVQWCDLGSLQPPPPGFRQFSCLSLPSSWDYRHVPPCPA-FCIFIEMEFYHVLQVGLELLTSGDPPA
          TQAGVQ.CDLGS.QPPPPGF..F.CLSL.SSWD...VP.CPA.F....E.....V.Q.GLELLT.GD.PA
Retrocopy TQAGVQ*CDLGSRQPPPPGFQRFFCLSLLSSWDNSYVPSCPAKFAFLVETRVFNVGQAGLELLTLGDLPA

Parental  LNSQSAGIIGVSH
          ..SQSA...GVSH
Retrocopy STSQSAETTGVSH

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

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3378 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3378 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3378 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,