RetrogeneDB ID: retro_cjac_1794

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:59089762..59090389(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINS3
• Ensembl ID: ENSCJAG00000011635
• Aliases: None
• Description: GINS complex subunit 3 (Psf3 homolog) [Source:HGNC Symbol;Acc:25851]

Sequence

>retro_cjac_1794
ATGTCCGGAGCTTATTTCCGGAAGGAGTCGGGTGCACTGGAGCCTGAGGAGAACTTTCTGTCCTTGCACGACATCCGGAT
GTCGCAGGAGACGCTCCCACTGCGCTCGTAGACCCGCCTGCCTCGCCTGGCGTTTTCTTCCTGGAGCGCAGGCGCAGAGA
CTGACAATGCAGTGCCGCCGCGCTCAAAGCCTGAACTCCCCTTGTGGCTGCAAAAGGACGTTTTGACAAGCGACGGATTC
GTTCTGTGGACTTCCCAAAATATAAGGGGAGGGTTGGAGGACCGTGTTCCGTGCGGATGCCAGTGTGACGGACCGCCACA
AAATGAGGCCCCATTTCTACGGGTTTGGCTCCCAGCTCCCGCATTTTGACAGTCTTGAGAATGCAACTATTTCCCAGTCT
CTGCTGCAGAACTTTTATTGGACTTGCCGCATCATGGACTCCTCCCCAAAAACTTACAACGGAGACACTTCAGCTCTGGT
AGCCAGGCTAGAAGAGATGGAGAGGGGCTTATTTCAAACAAGGCAGAAAGGACTGAATGACTTTCAGAGAAAGGGCAGGC
TTCTTGGATCACAGCTTCCAACCTCGTTTAGAATTACAAAAAGGGAAAATTCACTGACATGGAAGAA

Alignment

ORF - retro_cjac_1794 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSEAYFRVESGALGSEENFLSLDDILMSHEKLPVRMETAMPRLGAFFLERSGGAETDNAVPQGSKLELPL
          MS.AYFR.ESGAL..EENFLSL.DI.MS.E.LP.R..T..PRL...F...S.GAETDNAVP..SK.ELPL
Retrocopy MSGAYFRKESGALEPEENFLSLHDIRMSQETLPLRS*TRLPRLA--FSSWSAGAETDNAVPPRSKPELPL

Parental  WL-AKGLFDNKRRILSVE-LPKIYQEGWRTVFSADANVVDLHKIGPHFYGFGSQLLHFDSPENADISQSL
          WL.AKG.FD.KRRI.SV..LPKI..EGWRTVF.ADA.V.D.HK..PHFYGFGSQL.HFDS.ENA.ISQSL
Retrocopy WL<AKGRFD-KRRIRSVD<LPKI*GEGWRTVFRADASVTDRHKMRPHFYGFGSQLPHFDSLENATISQSL

Parental  LQTFIGRFRRIMDSSQNAYNEDTSALVARLDEMERGLFQTGQKGLNDFQCWEKG-QASQITVSTLVQNYK
          LQ.F.....RIMDSS...YN.DTSALVARL.EMERGLFQT.QKGLNDFQ...KG.QAS.IT.S.LV.NYK
Retrocopy LQNFYWTC-RIMDSSPKTYNGDTSALVARLEEMERGLFQTRQKGLNDFQ--RKG<QASWITASNLV*NYK

Parental  KRKFTDMED
          K.KFTDME.
Retrocopy KGKFTDMEE

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	0.07 RPM	1.02 RPM
SRP051959_heart	0.47 RPM	1.21 RPM
SRP051959_kidney	0.04 RPM	0.22 RPM
SRP051959_liver	0.09 RPM	0.11 RPM
SRP051959_lung	0.26 RPM	0.28 RPM
SRP051959_lymph_node	0.23 RPM	0.25 RPM
SRP051959_skeletal_muscle	0.09 RPM	0.04 RPM
SRP051959_spleen	0.36 RPM	0.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1794 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1794 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1794 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011635	1 retrocopy	retro_cjac_1794 ,