RetrogeneDB ID: retro_cjac_4062

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:49939295..49940521(+)
• Located in intron of: ENSCJAG00000000368

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX3X
• Ensembl ID: ENSCJAG00000009050
• Aliases: None
• Description: None

Sequence

>retro_cjac_4062
GGCTTTGGCAGATTTGAACGGAGTAGTCACAGTGGTTGGTGTGACAAGTCAGATGAAGATGATTGGTCAAACCACTTCCA
CCAAGTGAATGCTTGGAGCAGGAACAGTTTACTGAAGGAAATGCAGGGATTAGCTTTGAGAAATATGATGATATACCAGT
AGAAGCAACTGGCAGTAACTATCCTCCACACATTGAGAATTTCAGCGATATTGACATGGGAGAAATTATCATGGGTAACA
TTGAGCTTACTCACTATACTTGTCCTACTCCAGTGCAAAAACATACTATTCCTATTACTAACAGAAAAAGAGACTTAATG
GCTTGTGCCCAAACAGGTTCTGGGAAAACTGCAGCATTTCTTTTACCCATACTGAGTCAGATATATACAGATGGTCCAGG
AGAAGCTTTGAAGGCTGTGAAGAAAAATGGAAGGTATGGGTGCCGCAAAGAATACCCAATCTCCTTAGTTTTTGACCCAA
CAAGAGAATTGGCTGTACAGATCTATGAGGAAGCCAGACAATTTTCATACCAATCTAGAGTTCGTCCTTGTGTAGTTTAT
GGTGGTGCTGATATTGGTCAGCAGATTCAGGACTTAGAACGTGGATGCCACTTGTTAGTAGCCACTCCAGGACATCTAGT
GGATATGATGGAAAGAGGAAAGATTGGATTAGACTTCTGCAAATACTTAGTGTTGGATGAAGCTGATAGAATGATGGATG
TGAGATTTGAACCTTAGATACTTTGTATAATTGAACAAGATACTATGCCACTAAAGGGCATTCATCACACCATAATGTTT
AGCTCTACTTTTCCTTAGGAAATACAGTGCTTGCTCATGACTTTTTGGATGAATATATCTTTTTTGGCTGTAGGCAGAAT
AGGCTCTACCTCTGAGAACATCACACTCACACAGAAAGTAGTTTGGGTGGAAGATTTAGATAAATGGTCATTTCTGCTTG
ATCTCTTACATGCAACAGGGAGGGATTCACTGACTTCAGTGTTTGTGGAGACCAAAAAGGGAGTGGATTCTGTGGAGGAT
TTCTTATACCATGAAGGATATGTTTGTACTAGTATTCATGGAGACTGGTCACAGAGAGATCGAGAGGAGGCTTGTCACCA
GTTTCACTCAAGGAAAAGCCCAATTGTTGTGGCTACAGCTTTGGCAGCATGAGGACTAGACATTTCAAATGTGAGACATG
CTATCAATTTTGATTTGCCAAGTGAT

Alignment

ORF - retro_cjac_4062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.28 %
• Parental protein coverage: 63.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GFGKFERGGNSRWCDKSDEDDWS-KPLPPSERLEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIESFS
          GFG.FER...S.WCDKSDEDDWS.KPLPPSE.LEQE.F..GN.GI.FEKYDDIPVEATG.N.PPHIE.FS
Retrocopy GFGRFERSSHSGWCDKSDEDDWS<KPLPPSECLEQEQFTEGNAGISFEKYDDIPVEATGSNYPPHIENFS

Parental  DVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRA
          D..MGEIIMGNIELT.YT.PTPVQKH.IPI...KRDLMACAQTGSGKTAAFLLPILSQIY.DGPGEAL.A
Retrocopy DIDMGEIIMGNIELTHYTCPTPVQKHTIPITNRKRDLMACAQTGSGKTAAFLLPILSQIYTDGPGEALKA

Parental  MKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVAT
          .K.NGRYG.RK.YPISLV..PTRELAVQIYEEAR.FSY.SRVRPCVVYGGADIGQQI.DLERGCHLLVAT
Retrocopy VKKNGRYGCRKEYPISLVFDPTRELAVQIYEEARQFSYQSRVRPCVVYGGADIGQQIQDLERGCHLLVAT

Parental  PGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQ-ML
          PG.LVDMMERGKIGLDFCKYLVLDEADRM.D..FEP.I..I.EQDTMP.KG..HT.MFS.TFP.EIQ..L
Retrocopy PGHLVDMMERGKIGLDFCKYLVLDEADRMMDVRFEP*ILCIIEQDTMPLKGIHHTIMFSSTFP*EIQ<VL

Parental  ARDFLDEYI-FLAVGRVGSTSENI--TQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLED
          A.DFLDEYI.FLAVGR.GSTSENI..TQKVVWVE..DK.SFLLDLL.ATG.DSLT.VFVETKKG.DS.ED
Retrocopy AHDFLDEYI>FLAVGRIGSTSENITLTQKVVWVEDLDKWSFLLDLLHATGRDSLTSVFVETKKGVDSVED

Parental  FLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSD
          FLYHEGY.CTSIHGD.SQRDREEA.HQF.S.KSPI.VATA.AA.GLDISNV.H.INFDLPSD
Retrocopy FLYHEGYVCTSIHGDWSQRDREEACHQFHSRKSPIVVATALAA*GLDISNVRHAINFDLPSD

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	163.68 RPM
SRP051959_heart	0.00 RPM	215.46 RPM
SRP051959_kidney	0.00 RPM	286.73 RPM
SRP051959_liver	0.00 RPM	204.61 RPM
SRP051959_lung	0.00 RPM	257.40 RPM
SRP051959_lymph_node	0.00 RPM	230.95 RPM
SRP051959_skeletal_muscle	0.00 RPM	173.61 RPM
SRP051959_spleen	0.00 RPM	217.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4062 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4062 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4062 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035907	1 retrocopy	retro_btau_1846,
Callithrix jacchus	ENSCJAG00000009050	2 retrocopies	retro_cjac_1428, retro_cjac_4062 ,
Cavia porcellus	ENSCPOG00000013557	2 retrocopies	retro_cpor_326, retro_cpor_53,
Equus caballus	ENSECAG00000009901	1 retrocopy	retro_ecab_413,
Homo sapiens	ENSG00000215301	1 retrocopy	retro_hsap_4709,
Macaca mulatta	ENSMMUG00000017569	2 retrocopies	retro_mmul_1898, retro_mmul_2504,
Mus musculus	ENSMUSG00000000787	1 retrocopy	retro_mmus_205,
Ornithorhynchus anatinus	ENSOANG00000011274	1 retrocopy	retro_oana_64,
Pongo abelii	ENSPPYG00000020257	1 retrocopy	retro_pabe_3657,
Pan troglodytes	ENSPTRG00000022488	1 retrocopy	retro_ptro_3130,
Rattus norvegicus	ENSRNOG00000023383	1 retrocopy	retro_rnor_1415,