RetrogeneDB ID: retro_cjac_643

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:185274152..185274548(-)
• Located in intron of: ENSCJAG00000015845

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLRX2
• Ensembl ID: ENSCJAG00000008562
• Aliases: None
• Description: glutaredoxin 2 [Source:HGNC Symbol;Acc:16065]

Sequence

>retro_cjac_643
CCACCCACTAGAGCTCTCTCTGGGATGGAGAGCAACACATCCTCATCTTTGGAGAATTTAGCAACGGCACCTGTGAACCA
GATCCAAAAAACAATTTCCAATAATTGTGTGGTGATTTTCTCAAAAACATCCTGTTCTTACTGTACAATGGCAAAAAAGC
TTTTCCATGACATGAATGTTAACTATAAAGTGGTGGAATTGGACCTGCTTGAATATGGAAACCAGTTTCAAGATGCTCTT
TACAAAATGACTGGTGAAAGAACTGTTCCAAGAATATTTGTCAATGGTACCTTTATTGGAGGTGCAACTGACACTCATAG
GCTTCATAAAGAAGGAAAATTGCTTCCACTAGTTCATCAGCGTTATTTAAAAAAAAGTAAAAGGAAAGAATTTCAG

Alignment

ORF - retro_cjac_643 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 82.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRTRSAAWGMESNTSSSLENLATAPVNQIQETISNNCVVIFSKTSCSYCTMAKKLFHDMNVNYKVVELDL
          P.TR....GMESNTSSSLENLATAPVNQIQ.TISNNCVVIFSKTSCSYCTMAKKLFHDMNVNYKVVELDL
Retrocopy PPTRALS-GMESNTSSSLENLATAPVNQIQKTISNNCVVIFSKTSCSYCTMAKKLFHDMNVNYKVVELDL

Parental  LEYGNQFQDALYKMTGERTVPRIFVNGTFIGGATDTHRLHKEGKLLPLVHQCYLKKSKRKEFQ
          LEYGNQFQDALYKMTGERTVPRIFVNGTFIGGATDTHRLHKEGKLLPLVHQ.YLKKSKRKEFQ
Retrocopy LEYGNQFQDALYKMTGERTVPRIFVNGTFIGGATDTHRLHKEGKLLPLVHQRYLKKSKRKEFQ

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	0.27 RPM	3.17 RPM
SRP051959_heart	0.23 RPM	3.82 RPM
SRP051959_kidney	0.31 RPM	6.26 RPM
SRP051959_liver	0.15 RPM	4.72 RPM
SRP051959_lung	0.28 RPM	2.77 RPM
SRP051959_lymph_node	0.25 RPM	3.06 RPM
SRP051959_skeletal_muscle	0.04 RPM	3.82 RPM
SRP051959_spleen	0.19 RPM	3.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_643 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_643 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015972	1 retrocopy	retro_btau_543,
Choloepus hoffmanni	ENSCHOG00000007274	1 retrocopy	retro_chof_2375,
Callithrix jacchus	ENSCJAG00000008562	1 retrocopy	retro_cjac_643 ,
Equus caballus	ENSECAG00000015376	1 retrocopy	retro_ecab_169,
Felis catus	ENSFCAG00000025580	1 retrocopy	retro_fcat_733,
Myotis lucifugus	ENSMLUG00000015734	1 retrocopy	retro_mluc_1008,
Tupaia belangeri	ENSTBEG00000011216	1 retrocopy	retro_tbel_1638,
Drosophila melanogaster	FBgn0036820	1 retrocopy	retro_dmel_4,