RetrogeneDB ID: retro_cjac_379

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:1388300..1389446(+)
• Located in intron of: None

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_379
TGTTGGAAATGGGAGTTACTGATGGGAATTTTTTAAGTGGGCTTGGAAAAGTCATCTCCTATTCAGGAGGAGAGCATTCC
CATTGCTTTATCTGGTAGGGATATCTTAGCTAGAGCAAAAAATGGAACAGGCAAGAGCCATGCTTACCTCTTTTCCTTGC
TTGAATGGCTAGACCTGAAGAAAGACAATATACAAGCAGTGGTGATTGTTCCCACTGGAGACCTTGCTCTACAGGTCAGT
CAAATTTGCATCCATGACAGCAAACACGTGAGATGGGCCAAAGTGATTGTAATCACAGGGGGAACCAATTTAGGAGATGA
CACAATGAGGCTTGACGATACAATGCACGTGGTGATTGCTGCCCCTGGAGAATCCTGGATCTAATTAAGAAAGGAGTAGC
AAAGGTTGAATGCTGACCAGATGATAGCATTGATTGAGCAGGCAGATAAGTTGCTGTCACAGGATTTTGTGCAGATAATG
GAGTGTTTAATTCTCACAGTACCTAAAAACAGTCAGATTTTACTATATTCCACTACTTTCCCTCTTAATGTACAGAAGTT
CATGAGTTCCCAACTGCAGAACCCTATGAGATTAATCTAATGGAGGAACTAACTGTGACGAGAGTAACCCAGTACTCTGC
ATGTGTAACTGAGCACCAAAAAGTACACTGCCTCAACCCACTTTTCTCCAGGCTTCAGATAAACCAGTCGATCATTTTCT
GTAATTTCTCTCAGTGAGTTGAATTCCTAGCCAAGATTTCTCAACTGGGTTATTCTTGCTTCTATATCCATGCTAAAATG
AGGCAGGAACATCAAAATCATGTGTTTCATGATTTCCCAAAATGGCTTATGCCACGATCTTGTTGGCACTGATCTGTTTA
CCCGAGGTATTTCTATGCAAGCTGTTACTGTGATAATAAACTTCGATTTCCCAAACCTGGCAAAGACCCATCTCCATTGT
ATTGGAAGATCAAGTTGCTTTGGTCATGTTTGCTCAGCTATCAACTTGATGACATATGATGATCACTTCAACCTAAAAAA
TACTAAGGAGCAGCTGGGAACAGAAATTAAACTTATTCCAAGCAACATTGACAAGAGCCTGTATGTGGCAGAATACCACA
GCGAGCCTGTAGAAGATGAAAAACCT

Alignment

ORF - retro_cjac_379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.07 %
• Parental protein coverage: 79.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIV
          C.K.ELLMGIF..G.EK.SPIQEESIPIALSGRDILARAKNGTGKS.AYL..LLE.LDLKKDNIQA.VIV
Retrocopy CWKWELLMGIF*VGLEKSSPIQEESIPIALSGRDILARAKNGTGKSHAYLFSLLEWLDLKKDNIQAVVIV

Parental  PTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPG-RILDLIKKGVAKVD-H
          PT..LALQVSQICI..SKH...AKV...TGGTNL.DD.MRLDDT.HVVIA.PG.RILDLIKKGVAKV...
Retrocopy PTGDLALQVSQICIHDSKHVRWAKVIVITGGTNLGDDTMRLDDTMHVVIAAPG<RILDLIKKGVAKVE>A

Parental  VQMIVL-DEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQ-KPYEINLMEELTLK
          .QMI.L...ADKLLSQDFVQIME..ILT.PKN.QILLYS.TFPL.VQKFM.S.LQ..PYEINLMEELT..
Retrocopy DQMIALIEQADKLLSQDFVQIMECLILTVPKNSQILLYSTTFPLNVQKFMSSQLQ<EPYEINLMEELTVT

Parental  GVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVF
          .VTQY.A.VTE.QKVHCLN.LFSRLQINQSIIFCN.SQ.VE.LA.KISQLGYSCFYIHAKMRQEH.N.VF
Retrocopy RVTQYSACVTEHQKVHCLNPLFSRLQINQSIIFCNFSQ*VEFLA-KISQLGYSCFYIHAKMRQEHQNHVF

Parental  HDF-RNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNL
          HDF..NGLC..LV.TDLFTRGI..QAV.V.INFDFP.LA.T.LH.IGRS..FGH...AINL.TYDD.FNL
Retrocopy HDF>QNGLCHDLVGTDLFTRGISMQAVTVIINFDFPNLAKTHLHCIGRSSCFGHVCSAINLMTYDDHFNL

Parental  KSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPVEDEKP
          K...EQLGTEIK.IPSNIDKSLYVAEYHSEPVEDEKP
Retrocopy KNTKEQLGTEIKLIPSNIDKSLYVAEYHSEPVEDEKP

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	114.62 RPM
SRP051959_heart	0.00 RPM	133.48 RPM
SRP051959_kidney	0.00 RPM	119.43 RPM
SRP051959_liver	0.00 RPM	69.05 RPM
SRP051959_lung	0.00 RPM	187.12 RPM
SRP051959_lymph_node	0.00 RPM	197.43 RPM
SRP051959_skeletal_muscle	0.00 RPM	126.99 RPM
SRP051959_spleen	0.00 RPM	158.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_379 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_379 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1224
Pan troglodytes	retro_ptro_838
Pongo abelii	retro_pabe_1018
Macaca mulatta	retro_mmul_1300

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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,