RetrogeneDB ID: retro_cjac_477

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:155407046..155407508(+)
• Located in intron of: ENSCJAG00000017653

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIM39
• Ensembl ID: ENSCJAG00000020681
• Aliases: None
• Description: tripartite motif containing 39 [Source:HGNC Symbol;Acc:10065]

Sequence

>retro_cjac_477
ATGGCGGGGCTGGTTAAGGACCGCGAGGCCTTTCAGAGGCTCAACTTCCTGTACCAGGCCGCCCATTGTGTCCTTGCCCA
GGACCCCGAGAACCAGGCGCTGGCAAGATTTTACTGCCACACGGAGAGGACCATCGCGAAGCGGCTCGTCTTGCGGCGGG
ACCCTTTGGTGAAGAGGACTCTCTGTCGAGGTTGTTCTTCCCTCCTCGTCCCCGGCCTCACCTGCACCCAGCGCCAGAGA
CGCTGCAGGGGACAGCGCTGGACAGTACAGACCTGCCTAACATGCCAGCGCAGCCAACGCTTCCTCAATGATCCTGGGCA
TTTACTCTGGGGAGACAGGCCTGAGGCCCAGCTGGGGAACCAGACAGATACTAAACCACTACAGCCCTTGCCAAACGCAG
CCCACTCCATTCCAGCCCACCTTCCTGAGGAGAAAATGCCAACTCAAGGTTCCAGTCACCAG

Alignment

ORF - retro_cjac_477 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGPVKDREAFQRLNFLYQAAHCVLAQDPENQALARFYCHTERTIAKRLVLRRDPSVKRTLCRGCSSLLV
          MAG.VKDREAFQRLNFLYQAAHCVLAQDPENQALARFYCHTERTIAKRLVLRRDP.VKRTLCRGCSSLLV
Retrocopy MAGLVKDREAFQRLNFLYQAAHCVLAQDPENQALARFYCHTERTIAKRLVLRRDPLVKRTLCRGCSSLLV

Parental  PGLTCTQRQRRCRGQRWTVQTCLTCQRSQRFLNDPGHLLWGDRPEAQLGNQTDTKPLQPLPNAAHSTPAH
          PGLTCTQRQRRCRGQRWTVQTCLTCQRSQRFLNDPGHLLWGDRPEAQLGNQTDTKPLQPLPNAAHS.PAH
Retrocopy PGLTCTQRQRRCRGQRWTVQTCLTCQRSQRFLNDPGHLLWGDRPEAQLGNQTDTKPLQPLPNAAHSIPAH

Parental  LPEEKMPTQGSSHQ
          LPEEKMPTQGSSHQ
Retrocopy LPEEKMPTQGSSHQ

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	0.51 RPM	9.21 RPM
SRP051959_heart	0.12 RPM	9.75 RPM
SRP051959_kidney	0.84 RPM	10.92 RPM
SRP051959_liver	0.15 RPM	7.71 RPM
SRP051959_lung	0.31 RPM	11.09 RPM
SRP051959_lymph_node	0.59 RPM	11.14 RPM
SRP051959_skeletal_muscle	0.09 RPM	10.07 RPM
SRP051959_spleen	0.40 RPM	9.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_477 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_477 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_477 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010938	1 retrocopy	retro_cjac_1507,
Callithrix jacchus	ENSCJAG00000020681	1 retrocopy	retro_cjac_477 ,