RetrogeneDB ID: retro_cjac_426

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:78858367..78858722(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA7
• Ensembl ID: ENSCJAG00000014419
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 7 [Source:HGNC Symbol;Acc:9536]

Sequence

>retro_cjac_426
GGCCCCTGTGCCATCATGGTGGGTTTTGATGGCACCCCTCAACTCTATCAGGATGACCCCTCAGGCATGCACTGTACCTG
CAAGGCCAGTGCCATAGGCTGGACATCAAGGCAGTGAGTGAGTGCCTAGAGAAGAAGTAAGGGATGAAGCCATGGAAAGG
TGCCACCTGACCTTTAGGCTGGTGATGAAGACGCTCCTGGAAGTGGGTGCCTCAGGTGGCAGAAACATTGAAGTTGCTGT
CACCAGACGAGAGAAATCCCTTAGGAATTTACATTCTGAAGAAATTGGGATATATGTTGCTGAAATTGAAAAGGAAAAAG
AATAAAACAAAAAGAAGAAACAAAAGAAAGCATCA

Alignment

ORF - retro_cjac_426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.16 %
• Parental protein coverage: 54.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGA-KSVREFLEKN-YTDEAIETDDLTIKLVIKAL
          G..A..VGFD..GTP.LYQ.DPSG.....KA.AIG....K.V.E.LEK....DEA.E...LT..LV.K.L
Retrocopy GPCAIMVGFD--GTPQLYQDDPSGMHCTCKASAIGWTS<KAVSECLEKK<VRDEAMERCHLTFRLVMKTL

Parental  LEVVQSGGKNIELAVMRRDQPLKILNPEEIEKYVAEIEKEKEENEKKKQKKAS
          LEV..SGG.NIE.AV.RR...L..L..EEI..YVAEIEKEKE.N.KKKQKKAS
Retrocopy LEVGASGGRNIEVAVTRREKSLRNLHSEEIGIYVAEIEKEKE*NKKKKQKKAS

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	24.98 RPM
SRP051959_heart	0.02 RPM	15.05 RPM
SRP051959_kidney	0.00 RPM	25.82 RPM
SRP051959_liver	0.00 RPM	20.71 RPM
SRP051959_lung	0.00 RPM	18.04 RPM
SRP051959_lymph_node	0.00 RPM	23.22 RPM
SRP051959_skeletal_muscle	0.00 RPM	28.06 RPM
SRP051959_spleen	0.00 RPM	23.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_426 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_426 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_426 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014419	1 retrocopy	retro_cjac_426 ,
Felis catus	ENSFCAG00000003249	1 retrocopy	retro_fcat_1621,
Mus musculus	ENSMUSG00000027566	1 retrocopy	retro_mmus_407,
Rattus norvegicus	ENSRNOG00000008630	1 retrocopy	retro_rnor_2693,
Ictidomys tridecemlineatus	ENSSTOG00000012489	1 retrocopy	retro_itri_279,
Tupaia belangeri	ENSTBEG00000012281	2 retrocopies	retro_tbel_1048, retro_tbel_2392,
Drosophila melanogaster	FBgn0004066	1 retrocopy	retro_dmel_63,