RetrogeneDB ID: retro_cjac_2827

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:93801963..93802716(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA3
• Ensembl ID: ENSCJAG00000013395
• Aliases: None
• Description: None

Sequence

>retro_cjac_2827
ATGGCGGATGGCGAAGAGCCGGAGAAGAAAAGAAGGAGAGTAGAGGAGCTGCTGGCTGAGAAAATGGCTGTTGATGGTGG
GCGTGGGGACACTGGAGACTGGGAAGTCGCTAGAACCATGTAAAGAAGTTCCTCGAGTGATCTGGACCCTTCACACACCC
TGATTTCGAACCAAGCGCTGAATCTCTCCAGTTCTTGTTAGATACTTGTAAAGTTCTAGTCATTGGTGCTGGTGGCTTTA
GGATGTGATCTCCTGAAAAATCTGGCCCTGTCTGGTTTTAGACAGATTCATGTTACAGATATGGACACTATAGATGTTTC
CAATCTAAATAGGTAGCTTTTATTTAGACCTAAAGATGTTGGAAGACCTAAGGCTGAAGTTGCTGCAGAATTTCTAAATG
ACAGAGTTCCTGATTGCAATGTAGTTCCACATTTCAATAAGATTGAAGATTTTAACGACACTTTCTATCGACAATTTCAT
ATTATTGTCTGTGGACTGGACTCTATCATAGCCAGAAGATGGATAAATGGCATGCTGATCTCTCTTCTAAATTGTGAAGA
TGGTGTCTTAGATCCAAGCTCCGTTATCCCTTTGATAGATGGAGGGACAGAAGGTTTTAGAGGAAACGCCCAGGTGATTC
TGCCTGGAATGACTGCTTGTATCGAATTCACGCTGGAACTTTATCCACCACAGGTTAATTTTCCCATGTGCACCATTGCA
TCTATGCCCAGGCTACCAGAGCACTGTATTGAG

Alignment

ORF - retro_cjac_2827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.73 %
• Parental protein coverage: 54.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADGEEPEKKRRRIEELLAEKMAVDGGCGDSGDWE-GRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDT
          MADGEEPEKKRRR.EELLAEKMAVDGG.GD.GDWE..R.NHVKKFLE.SGPFTHPDFEPS.ESLQFLLDT
Retrocopy MADGEEPEKKRRRVEELLAEKMAVDGGRGDTGDWE<SR*NHVKKFLE*SGPFTHPDFEPSAESLQFLLDT

Parental  CKVLVIGAGG-LGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFSRPKDVGRPKAEVAAEFLNDRVP
          CKVLVIGAGG.LGC.LLKNLALSGFRQIHV.DMDTIDVSNLNR..LF.RPKDVGRPKAEVAAEFLNDRVP
Retrocopy CKVLVIGAGG>LGCDLLKNLALSGFRQIHVTDMDTIDVSNLNR*LLF-RPKDVGRPKAEVAAEFLNDRVP

Parental  NCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIIPLIDGGTEGFK
          .CNVVPHFNKI.DFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLN.EDGVLDPSS.IPLIDGGTEGF.
Retrocopy DCNVVPHFNKIEDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNCEDGVLDPSSVIPLIDGGTEGFR

Parental  GNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIE
          GNA.VILPGMTACIE.TLELYPPQVNFPMCTIASMPRLPEHCIE
Retrocopy GNAQVILPGMTACIEFTLELYPPQVNFPMCTIASMPRLPEHCIE

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	0.04 RPM	23.75 RPM
SRP051959_kidney	0.13 RPM	25.78 RPM
SRP051959_liver	0.06 RPM	15.79 RPM
SRP051959_lung	0.11 RPM	27.74 RPM
SRP051959_lymph_node	0.11 RPM	41.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	25.59 RPM
SRP051959_spleen	0.04 RPM	25.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2827 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2827 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010117	1 retrocopy	retro_amel_204,
Choloepus hoffmanni	ENSCHOG00000013626	2 retrocopies	retro_chof_1740, retro_chof_553,
Callithrix jacchus	ENSCJAG00000013395	2 retrocopies	retro_cjac_2827 , retro_cjac_2986,
Erinaceus europaeus	ENSEEUG00000005430	2 retrocopies	retro_eeur_374, retro_eeur_663,
Otolemur garnettii	ENSOGAG00000007771	2 retrocopies	retro_ogar_1868, retro_ogar_2776,
Rattus norvegicus	ENSRNOG00000006221	1 retrocopy	retro_rnor_852,
Sus scrofa	ENSSSCG00000011506	1 retrocopy	retro_sscr_192,