RetrogeneDB ID: retro_cjac_1428

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:87654736..87656027(-)
• Located in intron of: None

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_1428
CTGAACTCTTCAGATAATCAGAGTGGAGGAAGTACAGACAGCAAAGGGCGCTATATTCCTCCTCATTTAAGGAACCGAGA
AGCTACTAAAGGTTTCTACGATAAAGACAGTTCGGGGTGGAGTTCTAGCAAAGATAAGGATGCCTGTAGCAGTTTTGGAT
CTCGCAGTGATTCAAGAGGGAAGTCTAGCTTCTTCAGTGATCGTGGAAGTGGATCAAGGGGAAGCTTTGATGATCGTGGA
CGGAGTGATTATGACAACATTGGCAGCCGTGGTGACAGATGTGGCTTTGGCAAATTTGAACGTTGTGGAAACAGTCGCTG
GTGTGACCAATCAGATGAAGAAGATTGGTCAAAACCACTCCCACCAAGTGAACGCTTAGGACAGGAACTCTTTTCTGGAG
GCAACACTGGGATTAATCTTGAGAAATATGTTGACATTCCAGCTGAGGCCACAGGCAACAACTGTCCTCCACATATTGAA
AGTTTCAGTGATGTTGAGATGGGAGAAATTATCATGGGAAACATTGAGCTTACTCGTTACACTCACCCAACTCCAGTGCA
AAAGCATGCTATTCCTATTAAGAGAAAAGAGACTTGATGGCTTGTGCCCAAACAGGGGCGTGAAAAACTGCAGCATTTCT
CTCACCCATCTTGAGTCAGATTTATTCAGATGGTCCAGGCGAGGCTTTGAGGGCCATGAAGGAAAATGGAAGGTATGGGC
GCCGCAAACAGTACCTGATCTCCTTGATATTAGCACCAACGAGAGACTTGGCAGTACAGATCTACGAGGAAGCCAGAAAT
TTTTCATACCGATCTAGAGTTTGTCCTTGCGTGGTTTATGGTGGTGCCGATATTGGTCAGCAGATTTGAGACTTGGAACG
TGGATGCCACTTGTTAGTAGCCACTCCAGGACGTCTGGTGGATATGATGGAAAGAGGAAAGATTGGGTTAGACTTTTGCA
AATACGTGGTGTTAGATGAAGCTGATCAGATGTTGGGTATGGGTTTGAGCCTCAGAGACATAGAATAGTTGAACAAGATA
TTATGCCTCCAAAGGGTGTCCGCCACACTATGATGTTTAGTGCTACTTTTCCTAAAGAAATACAGATGCTGGCTCATGAT
TTATTAGATGAATATATCTTCTTGGCTGTAGGAATAGTTGGCTCTACCTCTGAAAACATCACATAGAAAGTAGTTTGGGT
CGAAGAATCAGACAAACAGTCATTTCTGCTTGACCTCCTAAATGCAACAGGCAAGGATTCACTGACCTTAGTGTTTGTGG
AGACCAAAAAG

Alignment

ORF - retro_cjac_1428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.47 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LNSSDNQSGGSTASKGRYIPPHLRNREATKGFYDKDSSGWSSSKDKDAYSSFGSRSDSRGKSSFFSDRGS
          LNSSDNQSGGST.SKGRYIPPHLRNREATKGFYDKDSSGWSSSKDKDA.SSFGSRSDSRGKSSFFSDRGS
Retrocopy LNSSDNQSGGSTDSKGRYIPPHLRNREATKGFYDKDSSGWSSSKDKDACSSFGSRSDSRGKSSFFSDRGS

Parental  GSRGRFDDRGRSDYDGIGSRGDRSGFGKFERGGNSRWCDKSDEDDWSKPLPPSERLEQELFSGGNTGINF
          GSRG.FDDRGRSDYD.IGSRGDR.GFGKFER.GNSRWCD.SDE.DWSKPLPPSERL.QELFSGGNTGIN.
Retrocopy GSRGSFDDRGRSDYDNIGSRGDRCGFGKFERCGNSRWCDQSDEEDWSKPLPPSERLGQELFSGGNTGINL

Parental  EKYDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEK-RDLMACAQTGSG
          EKY.DIP.EATGNNCPPHIESFSDVEMGEIIMGNIELTRYT.PTPVQKHAIP.IK.K.RDLMACAQTG..
Retrocopy EKYVDIPAEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTHPTPVQKHAIP-IKRK<RDLMACAQTGA*

Parental  KTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV
          KTAAFL.PILSQIYSDGPGEALRAMKENGRYGRRKQY.ISL.LAPTR.LAVQIYEEAR.FSYRSRV.PCV
Retrocopy KTAAFLSPILSQIYSDGPGEALRAMKENGRYGRRKQYLISLILAPTRDLAVQIYEEARNFSYRSRVCPCV

Parental  VYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDM-GFEPQIRRIVEQD
          VYGGADIGQQI.DLERGCHLLVATPGRLVDMMERGKIGLDFCKY.VLDEAD.ML.M.GFEPQ..RIVEQD
Retrocopy VYGGADIGQQI*DLERGCHLLVATPGRLVDMMERGKIGLDFCKYVVLDEADQMLGM<GFEPQRHRIVEQD

Parental  TMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNAT
          .MPPKGVRHTMMFSATFPKEIQMLA.D.LDEYIFLAVG.VGSTSENIT.KVVWVEESDK.SFLLDLLNAT
Retrocopy IMPPKGVRHTMMFSATFPKEIQMLAHDLLDEYIFLAVGIVGSTSENIT*KVVWVEESDKQSFLLDLLNAT

Parental  GKDSLTLVFVETKK
          GKDSLTLVFVETKK
Retrocopy GKDSLTLVFVETKK

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	0.11 RPM	163.68 RPM
SRP051959_heart	0.14 RPM	215.46 RPM
SRP051959_kidney	0.47 RPM	286.73 RPM
SRP051959_liver	0.09 RPM	204.61 RPM
SRP051959_lung	0.20 RPM	257.40 RPM
SRP051959_lymph_node	0.21 RPM	230.95 RPM
SRP051959_skeletal_muscle	0.15 RPM	173.61 RPM
SRP051959_spleen	0.17 RPM	217.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1428 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1428 has 0 orthologous retrocopies within eutheria group .

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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,