RetrogeneDB ID: retro_cjac_2307

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:2432981..2433379(+)
• Located in intron of: ENSCJAG00000010877

Retrocopy information

• Ensembl ID: ENSCJAG00000010934
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSME3
• Ensembl ID: ENSCJAG00000013111
• Aliases: None
• Description: proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki) [Source:HGNC Symbol;Acc:9570]

Sequence

>retro_cjac_2307
ATGGCCTCGTTGCTGAAGGTGGATCAGGAAGTGAAGCTCAAGGTTGATTCTTTCAGGGAGCAGATCACAAGAGAGGCAGA
CTTGATGGCAAATTTTTTCACAAAGAAGTTATTAGAACTTTATAGTTTTCTGAAGGAACCAATCTTAAACATCCATGATC
AAGCACAGATCCACTCTGACATGAGTCTCCCAGTCCCTGACCCCATTCTTCTCACCAATAGCCATGATGGACTGTATGGT
CGCACTTATAAGAAGCGAAGGTTGGATGAGTGTGAAGAAGCTTTCCAAGGAATCAAGGTGTTTGTCGTGCCCAATGGGAC
ACTGCAAAGCAACCAGCAGCTGGTGCACGTTATTGAGAAAGTGAAACCTGAGATCCGCTGTTGACTGAGAAATGTAAC

Alignment

ORF - retro_cjac_2307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.93 %
• Parental protein coverage: 50.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASLLKVDQEVKLKVDSFRERITSEAEDLVANFFPKKLLELDSFLKEPILNIHDLTQIHSDMNLPVPDPI
          MASLLKVDQEVKLKVDSFRE.IT.EA.DL.ANFF.KKLLEL.SFLKEPILNIHD..QIHSDM.LPVPDPI
Retrocopy MASLLKVDQEVKLKVDSFREQITREA-DLMANFFTKKLLELYSFLKEPILNIHDQAQIHSDMSLPVPDPI

Parental  LLTNSHDGLDGPTYKKRRLDECEEAFQGTKVFVMPNGMLKSNQQLVDIIEKVKPEIR-LLIEKCN
          LLTNSHDGL.G.TYKKRRLDECEEAFQG.KVFV.PNG.L.SNQQLV..IEKVKPEIR.LL.EKCN
Retrocopy LLTNSHDGLYGRTYKKRRLDECEEAFQGIKVFVVPNGTLQSNQQLVHVIEKVKPEIR<LLTEKCN

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	17.42 RPM
SRP051959_heart	0.07 RPM	12.26 RPM
SRP051959_kidney	0.00 RPM	17.99 RPM
SRP051959_liver	0.00 RPM	10.87 RPM
SRP051959_lung	0.03 RPM	12.30 RPM
SRP051959_lymph_node	0.02 RPM	14.98 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.02 RPM
SRP051959_spleen	0.00 RPM	14.22 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2307 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2307 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2307 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
Anolis carolinensis	ENSACAG00000013688	2 retrocopies	retro_acar_118, retro_acar_37,
Bos taurus	ENSBTAG00000019918	2 retrocopies	retro_btau_1249, retro_btau_941,
Callithrix jacchus	ENSCJAG00000007167	3 retrocopies	retro_cjac_233, retro_cjac_322, retro_cjac_71,
Callithrix jacchus	ENSCJAG00000013111	1 retrocopy	retro_cjac_2307 ,
Cavia porcellus	ENSCPOG00000012552	1 retrocopy	retro_cpor_1204,
Equus caballus	ENSECAG00000012620	2 retrocopies	retro_ecab_29, retro_ecab_827,
Homo sapiens	ENSG00000131467	1 retrocopy	retro_hsap_245,
Loxodonta africana	ENSLAFG00000013446	1 retrocopy	retro_lafr_725,
Mustela putorius furo	ENSMPUG00000010027	1 retrocopy	retro_mputfur_619,
Oryctolagus cuniculus	ENSOCUG00000015986	1 retrocopy	retro_ocun_641,
Pongo abelii	ENSPPYG00000008372	1 retrocopy	retro_pabe_413,
Pan troglodytes	ENSPTRG00000009225	1 retrocopy	retro_ptro_212,
Sus scrofa	ENSSSCG00000017385	1 retrocopy	retro_sscr_784,
Ictidomys tridecemlineatus	ENSSTOG00000028833	1 retrocopy	retro_itri_153,