RetrogeneDB ID: retro_cjac_1924

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:74177589..74178491(-)
• Located in intron of: ENSCJAG00000014433

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX6
• Ensembl ID: ENSCJAG00000013591
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 6 [Source:HGNC Symbol;Acc:2747]

Sequence

>retro_cjac_1924
CAAATTTGCATCCAGGTCAGCAAACACATGGGAGGGGTCAAAGTGATGGCAACCATCGGAGGAACCAATTTACGAGATGA
CATAATGAGGCTTGATGATACAGTGCATGTGGTGATTGCTACGCCTGGGAGAATCCTGGATCTTATTAAGAAAGGAATAG
CAAAGGTTGATCATGTCCAGATGATAGTATTAGATGAGGCAGATAAGTTGCTGTCACAGGATTTTGTGCAGATAATGGAG
GATATTATTCTCACGCTACCTAAAAACAGGCAGATTATATTCCGCTACTTTCCCTCTTAGTGTACAGAAGTTCATGAATT
CCCATTTACAGAAACCCTACGAGATTAACCTGATGGAAAATACTAACTCTAAAGGGAGTAACCCAGTACTACGCATATGT
AACTGAGTGCCAAAAAGTACACTGCCTCAACACACTTTTCTCCAGGCTTCAGAAATACCAGTCGATCATTTTCTGTAACT
CCTCTCAGCGAGTTGAATTGCTAGCCAAGAAGATTTCTCAACTGGGTTATCCTTGCTTCTATATTCATGCTAAAATAAGG
CAGGAACATCAAAATCGTGTATTTCATGATTTCTGAAATGGCTTATGCCACAATCTTGTTTGCACGGATCTGTTTACCCG
AGGTATTGATATACAAGCTGTGAATGTGGTAATAAACTTTGATTTCCCAAAGCTGGCAGAGACCTATCTCCATCATATTG
GAAGATCAGGTCGCTTTGGTCATCTTGGCTTAGCCATCAACTTGATCACATATGATGATTGCTTCAATCTGAAAAGTATT
GAGGAGCAGCTGGGAACAGAAATTAAACCTATTGTAAGCAACACTGACAAGAGCCTGTATGTGGCAGAATACCACAGCGA
GCCTGTAGAAGATGAGATACCT

Alignment

ORF - retro_cjac_1924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.78 %
• Parental protein coverage: 62.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKL
          QICIQVSKHMGG.KVMAT.GGTNLRDDIMRLDDTVHVVIATPGRILDLIKKG.AKVDHVQMIVLDEADKL
Retrocopy QICIQVSKHMGGVKVMATIGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGIAKVDHVQMIVLDEADKL

Parental  LSQDFVQIMEDIILTLPKNRQILLYSATFP-LSVQKFMNSHLQKPYEINLMEE-LTLKGVTQYYAYVTER
          LSQDFVQIMEDIILTLPKNRQI......FP.LSVQKFMNSHLQKPYEINLME..LTLKGVTQYYAYVTE.
Retrocopy LSQDFVQIMEDIILTLPKNRQIIF--RYFP>LSVQKFMNSHLQKPYEINLMEN>LTLKGVTQYYAYVTEC

Parental  QKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLV
          QKVHCLNTLFSRLQ..QSIIFCNSSQRVELLAKKISQLGY.CFYIHAK.RQEH.NRVFHDF.NGLC.NLV
Retrocopy QKVHCLNTLFSRLQKYQSIIFCNSSQRVELLAKKISQLGYPCFYIHAKIRQEHQNRVFHDF*NGLCHNLV

Parental  CTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKP
          CTDLFTRGIDIQAVNVVINFDFPKLAETYLH.IGRSGRFGHLGLAINLITYDD.FNLKSIEEQLGTEIKP
Retrocopy CTDLFTRGIDIQAVNVVINFDFPKLAETYLHHIGRSGRFGHLGLAINLITYDDCFNLKSIEEQLGTEIKP

Parental  IPSNIDKSLYVAEYHSEPVEDEKP
          I.SN.DKSLYVAEYHSEPVEDE.P
Retrocopy IVSNTDKSLYVAEYHSEPVEDEIP

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	0.87 RPM	114.62 RPM
SRP051959_heart	0.65 RPM	133.48 RPM
SRP051959_kidney	0.64 RPM	119.43 RPM
SRP051959_liver	0.50 RPM	69.05 RPM
SRP051959_lung	1.25 RPM	187.12 RPM
SRP051959_lymph_node	2.47 RPM	197.43 RPM
SRP051959_skeletal_muscle	0.83 RPM	126.99 RPM
SRP051959_spleen	1.30 RPM	158.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1924 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1924 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1924 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012442	1 retrocopy	retro_cfam_1347,
Callithrix jacchus	ENSCJAG00000013591	3 retrocopies	retro_cjac_1427, retro_cjac_1924 , retro_cjac_379,
	ENSG00000110367	0 retrocopies
Gorilla gorilla	ENSGGOG00000016751	1 retrocopy	retro_ggor_955,
Macaca mulatta	ENSMMUG00000018651	2 retrocopies	retro_mmul_1300, retro_mmul_1826,
Mus musculus	ENSMUSG00000032097	1 retrocopy	retro_mmus_1896,
Nomascus leucogenys	ENSNLEG00000007372	1 retrocopy	retro_nleu_695,
Otolemur garnettii	ENSOGAG00000007978	1 retrocopy	retro_ogar_2861,
Pongo abelii	ENSPPYG00000003942	2 retrocopies	retro_pabe_1018, retro_pabe_2941,
Pan troglodytes	ENSPTRG00000004353	2 retrocopies	retro_ptro_2424, retro_ptro_838,
Rattus norvegicus	ENSRNOG00000012453	4 retrocopies	retro_rnor_2546, retro_rnor_2613, retro_rnor_900, retro_rnor_901,