RetrogeneDB ID: retro_cjac_1200

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:41409686..41410307(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB12
• Ensembl ID: ENSCJAG00000007303
• Aliases: None
• Description: None

Sequence

>retro_cjac_1200
AGGAAGTAGTATGACCATTTCAGTGATAACAGGAGCCAGGTAGCCCGGCCCAGCTATGGGCATGGGGACTTCCACCATGG
CTTTGAGGCTGACATCTCCCCTGAAGACCTCTTCAACATGTTCTTTGGTGGTGGCTTCCCTTCTAGTAAAGTCCACATCT
ACAGCAACAGCCACATGTGCTATACATACCAGTAAAGGCGGGACCGCATGGAGAACCAGGGTGATGATGGGCGAGGGGTG
TTTGTGCAGCTGATGCCCATCCTCATCCTGATCCTCGTGTCAGTTCTCAGCCAGTTCATGGTCTCCAGTTCACCCTTCAG
TCTGAGCCTAAGACCGTCTGTGAGCCACATCACAGGTGAGTCACACCTGAGTGTCATTTCCTATGTGGCAGACAATTTCT
CCAAGGAGTACACAGGCTCCAGTCTCAAAGCAGTCAAACCAAATGTGGAAGATGATTACATCGCCAACCTCTGGAACAAC
TGCTGGAAGGAGAAGCAGCAGAACGAAGGCTTTCTGTACTGGGACCGCTACTTTGGCGACACAGTTATGTACCACAAAGC
ACAGGAGATGGGCACCCCCTGCTGCAGCCAACTGTCAGAGGTGCAGGCCTCCCTGCATGGA

Alignment

ORF - retro_cjac_1200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.56 %
• Parental protein coverage: 50.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKQYDQFGDDKSQAARHGHGHGDFHRGFEADISPEDLFNMFFGGGFPSSNVHVYSNGRMRYTYQQRQDRR
          RK.YD.F.D..SQ.AR...GHGDFH.GFEADISPEDLFNMFFGGGFPSS.VH.YSN..M.YTYQ.R.DR.
Retrocopy RK*YDHFSDNRSQVARPSYGHGDFHHGFEADISPEDLFNMFFGGGFPSSKVHIYSNSHMCYTYQ*RRDRM

Parental  ENQGDGGLGVFVQLMPILILILVSALSQLMVSSPPYSLSPRPSVGHIHRRVTDHLSVVYYVGDTFSEEYT
          ENQGD.G.GVFVQLMPILILILVS.LSQ.MVSS.P.SLS.RPSV.HI......HLSV..YV.D.FS.EYT
Retrocopy ENQGDDGRGVFVQLMPILILILVSVLSQFMVSSSPFSLSLRPSVSHITGE--SHLSVISYVADNFSKEYT

Parental  GSSLKTVERNVEDDYIANLRNNCWKEKQQKEGLLYRARYFGDTDMYHKAQKMGTPSCSRLSEVQASLHG
          GSSLK.V..NVEDDYIANL.NNCWKEKQQ.EG.LY..RYFGDT.MYHKAQ.MGTP.CS.LSEVQASLHG
Retrocopy GSSLKAVKPNVEDDYIANLWNNCWKEKQQNEGFLYWDRYFGDTVMYHKAQEMGTPCCSQLSEVQASLHG

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	10.23 RPM
SRP051959_heart	0.00 RPM	15.63 RPM
SRP051959_kidney	0.02 RPM	18.06 RPM
SRP051959_liver	0.00 RPM	16.92 RPM
SRP051959_lung	0.00 RPM	15.65 RPM
SRP051959_lymph_node	0.00 RPM	11.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	21.14 RPM
SRP051959_spleen	0.00 RPM	14.43 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1200 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1200 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2273
Pan troglodytes	retro_ptro_1608
Gorilla gorilla	retro_ggor_1691
Pongo abelii	retro_pabe_1945

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007303	1 retrocopy	retro_cjac_1200 ,
Dasypus novemcinctus	ENSDNOG00000009977	1 retrocopy	retro_dnov_866,
Homo sapiens	ENSG00000148719	1 retrocopy	retro_hsap_2273,
Gorilla gorilla	ENSGGOG00000000683	1 retrocopy	retro_ggor_1691,
Macropus eugenii	ENSMEUG00000002024	2 retrocopies	retro_meug_1115, retro_meug_1511,
Pongo abelii	ENSPPYG00000002353	1 retrocopy	retro_pabe_1945,
Pan troglodytes	ENSPTRG00000002613	1 retrocopy	retro_ptro_1608,