RetrogeneDB ID: retro_cjac_995

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:84060913..84062673(+)
• Located in intron of: ENSCJAG00000036372

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKD3
• Ensembl ID: ENSCJAG00000003965
• Aliases: None
• Description: None

Sequence

>retro_cjac_995
GATTGTAAATTCAACTGTTTTACATGCTGTGCATCAAAAGTACCAAGAGACTGCCTGGAGAGGTTACTTTCATGGAGAAC
CTTCGAATCTGGGAACAGATACAGATATACCAACAGATATTGACAATAATGACATAAATAGTGATAGCAGTAGGGGCTTG
GATGACATGGAAGAGCAATCTCCCCCAGAAGACAAGATGTTCTTCCTGGAACTATCTGATCTTGATGTGGAAAGAAGTAA
AGAAGCCATTAAAACAATCAGTCCATCAACAGGCAATAATATTCTGCTAATGAGCGTTGTACAATCCATCAAGTACACAA
AGACGAAGAGCAGCACCATGGTGAAGGAAGGGTGGATGGTCCATTACACCAGCAGGGATAACCTGAGAAAGAGGCATTAC
TGGAGACTTGACAGCAAATGAGTAACATTATTTTCAGAATGAATCTGGATCAAAGTATTGTAAGAAAATTCCACTTTTAG
AAATTCTTCACATATCTTCACCAAGAGATTTCATAAACATTTCACAAGGCAGCAATCCACACTGTTTTGAAATCATCACT
GATACTATGATATACTTCGTTGGTGAGAACAATGGGGATAGCTCTCATAATCCTCTTTTTGCTGCTACTGGAGTTGGACT
TGATGTAGCATAGAGCTGGGAAAAAGCAATTCGCCAAGCCCTCATGCCTGTTACTCCTCAAACAAGTGTTTGTACTTCTC
CATGGCAAGGGAAAGATCACAAAGATTTGTCCATGAGTATCTCTGTATCTAATTGTCAGATCCAGGAGAATGTGCATAAC
AGTACTGTTTACCAGATCTTTGCAGATGAAGTGCTTGGTTCAGGCCAGTTTGGCATTGTTTATGGAGGAAAACCTAGAAA
GACTGGAAGGGATGTGGCTATTAAAGTAACTGATGAGATGAGATTCCCCACAAAACAAGAAAGTCAACTCCAAAATGAAG
TGGCTATTTTCCAGAATTTGCACCATCCTGGGATTGTAAACCTGTAATGTATGTTTGAAACCCCAGAATGAGTCTTTGTA
GTCATGGAAAAGCTGCATGGCGTTATGTTGGAAATGATTCTATCTAGTGAGAAAAGTCGGCTTCCAGAACGAGTTACTAA
ATTCATGGTCACACAGATACTTGTTGCTTTGAGGCATCTGCATTTTAAGAATATTGTGCACTGTGATTTAAAGCCAGAAA
ATGTGCTGCTTGCATCAGCAGAGCCATTTCCTCAGGTGAAGTTGTGTGATTTTGGATTTGCATGCATCATTGTTGAAAAG
TCATTCAGGAGCTCTGTGGTAGGAACTCCAGCATACTTAGCCCCTGAAGTTCTCTGGATTAAAGGTTACAACCGTTCCCT
AGATATGTGGTCAGTGGGAGTTATCATCTATGTGAGCCTCAGTGGCACGTTTCCTTTTCATGAGGATGAAGATATAAATG
ATCAGATCCAAAATGCCGCGTTTACATACCCGCCAAATCCATGGAAAGAAATTTCTGGTGAAGCAATTGATTTGATAAAC
AATCTGCTTCAAGTGAAGATGAGAAAGCATTAGAGTATTGACATATCTCTTAGTCATCCCCGGCTACAGGACTATCACAC
TTGGCTTGACCTTAGAGAATTTGAAACTCGCATTGAAGAACGTTACATTACACATGAAAGTGATGATGTTCGCTGGGAAA
TACATGCATACACACATAACCTTGTACACCCAAAGCACTTCATTATGGCTTCTAATCCAGATGATATGGAAGAAGATCCT

Alignment

ORF - retro_cjac_995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.32 %
• Parental protein coverage: 65.96 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DCKFNCHKRCASKVPRDCL-GEVTF-NGEPSSLGTDTDIPMDIDNNDINSDSSRGLDDTEEPSPPEDKMF
          DCKFNC...CASKVPRDCL.GEVTF..GEPS.LGTDTDIP.DIDNNDINSDSSRGLDD.EE.SPPEDKMF
Retrocopy DCKFNCFTCCASKVPRDCL<GEVTF<HGEPSNLGTDTDIPTDIDNNDINSDSSRGLDDMEEQSPPEDKMF

Parental  FLDPSDLDVERDEEAVKTISPSTSNNIPLMRVVQSIKHTKRKSSTMVKEGWMVHYTSRDNLRKRHYWRLD
          FL..SDLDVER..EA.KTISPST.NNI.LM.VVQSIK.TK.KSSTMVKEGWMVHYTSRDNLRKRHYWRLD
Retrocopy FLELSDLDVERSKEAIKTISPSTGNNILLMSVVQSIKYTKTKSSTMVKEGWMVHYTSRDNLRKRHYWRLD

Parental  SKCLTLF-QNESGSKYYKEIPLSEILRISSPRDFTNISQGSNPHCFEIITDTMVYFVGENNGDSSHNPVL
          SK..TLF.QNESGSKY.K.IPL.EIL.ISSPRDF.NISQGSNPHCFEIITDTM.YFVGENNGDSSHNP..
Retrocopy SK*VTLF>QNESGSKYCKKIPLLEILHISSPRDFINISQGSNPHCFEIITDTMIYFVGENNGDSSHNPLF

Parental  AATGVGLDVAQSWEKAIRQALMPVTPQASVCTSPGQGKDHKDLSMSISVSNCQIQENVDISTVYQIFADE
          AATGVGLDVA.SWEKAIRQALMPVTPQ.SVCTSP.QGKDHKDLSMSISVSNCQIQENV..STVYQIFADE
Retrocopy AATGVGLDVA*SWEKAIRQALMPVTPQTSVCTSPWQGKDHKDLSMSISVSNCQIQENVHNSTVYQIFADE

Parental  VLGSGQFGIVYGGKHRKTGRDVAIKVIDKMRFPTKQESQLRNEVAILQNLHHPGIVNLECMFETPERVFV
          VLGSGQFGIVYGGK.RKTGRDVAIKV.D.MRFPTKQESQL.NEVAI.QNLHHPGIVNL.CMFETPE.VFV
Retrocopy VLGSGQFGIVYGGKPRKTGRDVAIKVTDEMRFPTKQESQLQNEVAIFQNLHHPGIVNL*CMFETPE*VFV

Parental  VMEKLHGDMLEMILSSEKSRLPERITKFMVTQILVALRNLHFKNIVHCDLKPENVLLASAEPFPQVKLCD
          VMEKLHG.MLEMILSSEKSRLPER.TKFMVTQILVALR.LHFKNIVHCDLKPENVLLASAEPFPQVKLCD
Retrocopy VMEKLHGVMLEMILSSEKSRLPERVTKFMVTQILVALRHLHFKNIVHCDLKPENVLLASAEPFPQVKLCD

Parental  FGFARIIGEKSFRRSVVGTPAYLAPEVLRSKGYNRSLDMWSVGVIIYVSLSGTFPFNEDEDINDQIQNAA
          FGFA.II.EKSFR.SVVGTPAYLAPEVL..KGYNRSLDMWSVGVIIYVSLSGTFPF.EDEDINDQIQNAA
Retrocopy FGFACIIVEKSFRSSVVGTPAYLAPEVLWIKGYNRSLDMWSVGVIIYVSLSGTFPFHEDEDINDQIQNAA

Parental  FMYPPNPWKEISGEAIDLINNLLQVKMRKRYSVDKSLSHPWLQDYQTWLDLREFETRIGERYITHESDDA
          F.YPPNPWKEISGEAIDLINNLLQVKMRK..S.D.SLSHP.LQDY.TWLDLREFETRI.ERYITHESDD.
Retrocopy FTYPPNPWKEISGEAIDLINNLLQVKMRKH*SIDISLSHPRLQDYHTWLDLREFETRIEERYITHESDDV

Parental  RWEIHAYTHNLVYPKHFIMAPNPDDMEEDP
          RWEIHAYTHNLV.PKHFIMA.NPDDMEEDP
Retrocopy RWEIHAYTHNLVHPKHFIMASNPDDMEEDP

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	33.21 RPM
SRP051959_heart	0.00 RPM	31.48 RPM
SRP051959_kidney	0.00 RPM	24.96 RPM
SRP051959_liver	0.00 RPM	18.50 RPM
SRP051959_lung	0.02 RPM	47.89 RPM
SRP051959_lymph_node	0.00 RPM	53.95 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.12 RPM
SRP051959_spleen	0.04 RPM	40.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_995 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_995 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_995 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003965	1 retrocopy	retro_cjac_995 ,
Callithrix jacchus	ENSCJAG00000011801	1 retrocopy	retro_cjac_573,