RetrogeneDB ID: retro_cjac_3309

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:64030765..64031236(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINS2
• Ensembl ID: ENSCJAG00000017303
• Aliases: None
• Description: GINS complex subunit 2 (Psf2 homolog) [Source:HGNC Symbol;Acc:24575]

Sequence

>retro_cjac_3309
GGCGAGGGAACTGGAGCCTTTTAACCCAGGTTTGGTTTACCAATGGAAGTGCCCTGTAGCTGGCAATTAACCTGAAACAA
AGACAGAAATGTCAGCTGCTCCCTCCGGAGTGGACGGATATAGAAAAGCTGGAGAAGATGAGGGATCATGAACGAAAGGA
ACATTTACCTACCCCAATGCCCAGCCCTTACTACATGGATCTTACCAAGCTGCTGTTAATCATACTTCAGACAACATCCC
GAACACAGGAGAAATCCCGATCCTGGTCAAGGATATGTGGGACACTTATATAGCCAGCCTTCGAGTGTCTGCTGACAGCT
TTGTGAGACAGCACTAAGCACATGCCAAGCTGGATAACTTGACCTTGATGGAGATCAACAGCAGTGGGACTTTCCTCACG
CAAGCACTCAACCACTGTAGAAACTGCGCACAAACCTCCAGCTTTCGGAGAGTACCCAGTCTCAGGACTTC

Alignment

ORF - retro_cjac_3309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.88 %
• Parental protein coverage: 84.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGDLGPFNP--GLPVEVP-LWLAINLKQRQKCRLLPPEWMDVEKLEKIRDHERKEETFTPMPSPYYMELT
          G...G.F.P..GLP.EVP.L.LAINLKQRQKC.LLPPEW.D.EKLEK.RDHERKE...TPMPSPYYM.LT
Retrocopy GEGTGAF*PRFGLPMEVP<L*LAINLKQRQKCQLLPPEWTDIEKLEKMRDHERKEHLPTPMPSPYYMDLT

Parental  KLLL-NHASDNIPKADEIRTLVKDMWDTRIAKLRVSADSFVRQQEAHAKLDNLTLMEINTSGTFLTQALN
          KLLL.NH.SDNIP...EI..LVKDMWDT.IA.LRVSADSFVRQ..AHAKLDNLTLMEIN.SGTFLTQALN
Retrocopy KLLL<NHTSDNIPNTGEIPILVKDMWDTYIASLRVSADSFVRQH*AHAKLDNLTLMEINSSGTFLTQALN

Parental  H-MYKLRTNLQPSESTQSQDF
          H...KLRTNLQ.SESTQSQDF
Retrocopy H<L*KLRTNLQLSESTQSQDF

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	0.60 RPM
SRP051959_heart	0.00 RPM	0.26 RPM
SRP051959_kidney	0.00 RPM	0.09 RPM
SRP051959_liver	0.04 RPM	0.13 RPM
SRP051959_lung	0.00 RPM	0.47 RPM
SRP051959_lymph_node	0.00 RPM	0.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.09 RPM
SRP051959_spleen	0.00 RPM	0.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3309 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3309 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017303	1 retrocopy	retro_cjac_3309 ,
Dasypus novemcinctus	ENSDNOG00000008760	4 retrocopies	retro_dnov_1034, retro_dnov_166, retro_dnov_2424, retro_dnov_604,
Homo sapiens	ENSG00000131153	1 retrocopy	retro_hsap_2477,
Gallus gallus	ENSGALG00000028131	1 retrocopy	retro_ggal_22,
Gorilla gorilla	ENSGGOG00000009069	2 retrocopies	retro_ggor_1542, retro_ggor_960,
Macropus eugenii	ENSMEUG00000014703	1 retrocopy	retro_meug_1479,
Microcebus murinus	ENSMICG00000016691	1 retrocopy	retro_mmur_342,
Macaca mulatta	ENSMMUG00000020594	1 retrocopy	retro_mmul_596,
Pongo abelii	ENSPPYG00000007616	2 retrocopies	retro_pabe_1826, retro_pabe_896,
Pan troglodytes	ENSPTRG00000008430	1 retrocopy	retro_ptro_1433,
Pteropus vampyrus	ENSPVAG00000004944	1 retrocopy	retro_pvam_762,
Sarcophilus harrisii	ENSSHAG00000015249	1 retrocopy	retro_shar_382,
Sus scrofa	ENSSSCG00000002663	1 retrocopy	retro_sscr_883,
Tupaia belangeri	ENSTBEG00000006220	1 retrocopy	retro_tbel_1328,