RetrogeneDB ID: retro_cjac_961

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:31434434..31435918(+)
• Located in intron of: ENSCJAG00000016278

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK16
• Ensembl ID: ENSCJAG00000012261
• Aliases: None
• Description: cyclin-dependent kinase 16 [Source:HGNC Symbol;Acc:8749]

Sequence

>retro_cjac_961
GCCGTGGATCATATGAAGATCAGACAGCAGCTGTTAATGACACTCTGAGGTAGCCGAAGCATAGAGAAGACCAATGGTGC
CACTGAGCAGATAGGCCGGGATGAGAGTGGTGGTGGTGGTGGCAGTGACCCTGGAGAGGCCCCCACACGTGCTGCTCGTG
GAGAACTTCGCTCTACACAGGGCCCACTCAGCTCTGCACCAGAGATTGTGCACGAGGACTTGAAGATGGGGTCTGATGGG
GAGAGTGACCAGGCTTCAGCCACATTCTCAGACGAGGTGCAGTCTCCAGTGAGAGTGCCCATGCACAACCATCCCCCATG
CAAGATCTCCACTGAGGACATCAACAAGCACCTATCACTACCAGCTGACACCTGGCTACCTGAGAGCTACCTTGAGAAGC
TGACCCTCAATAGCCCCATCTTTGACAAGTCACTCAGCCGCCGCCTCCATCATGTCAGCCTGTCTGAGACTGGCTTTGGG
AAACTGGAGACTTACATTAAGCTGGACAACGTGGGCGAGGGTACCTATGCCACCGTCTACAAAGGCAAAAGCTCACAGAC
AACCTTGTGGTGCTCAAGGAGACCAGACTGGAACATGGAGAGGGGACACCGTGCACGGCCATCAGGGAAGTGTCTCTACT
CAAGGACCTCAAACACGCCAACATTGTTATGGTACGTGACATAATCCACCTGGAGAAGTCCCTCTCCCTTGTCTTTGAGT
ACCTGGACAAGGACCTCAAGCAGTACCTGGATGACTGTGGGAACATCATCAACATGCACAATATGAAACTGTTCCTGTTC
CAGCTGCTCCATGGCCTGGCCTACTGCCACCAGCAGAAGGTACTACACTGAGACCTCAAGCCCCAGAACCTGCTCATCAA
TGAGAGAGGAGAGCTCAAGCTGGCTGACTTTGGTCTGGCCCGAGCCAAGTCAATCCCAACAAAGATGTACTCCAATGAGG
TGGGGACACTGTGGTACTGTCCCCTGACATCCTGCTTGGGTCCACGGACTACTCTACTCAGATTGACATGTGGCGTGTGG
GCTGCATCTTCTATGAGATGGCCACAGGCTGGGCCCTCTTCCCGGGCTCCATGGTGGAGGAACAACTGCATTTCATCTTC
CACATCTTAGGAACCCCAACTGAGGAGACGTGGCCAGGCATCCTGTCCAATAAGAAGTTCAAGACCTACAACTACCCCAA
GTACCAAGCCGAGGCCTTTTTGAGCCACACACCCCGACTTGATAGTGATGGGACTGACCTCCTTACCAAGCTGCTGCAGT
TTGAGGGTCGAAATCGGATCTCTGCAGAGGATGCCATGAAACATCCATTCTTCCTTGGTCTGGGGGAGCGGATCCACAAA
CTTCCTGACACTTCTTCCATATTTGCACTAAAGGAGATTCAGCTACAAAAGGAGGACAGCCTTCGGTCTTCATCAATGCC
TGACTCAGGCAGGCCAGCTTTTCCGCGTGGTGGACACCGAGTTC

Alignment

ORF - retro_cjac_961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.63 %
• Parental protein coverage: 99.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AMDRMKKIKRQLSMTLRGSRNIDKTNGATEQIGLDESGGGGGGSDPGEAPTRAAPGELRSARGPLSSAPE
          A.D.MK.I..QL.MTL.GSR.I.KTNGATEQIG.DESGGGGG.SDPGEAPTRAA.GELRS..GPLSSAPE
Retrocopy AVDHMK-IRQQLLMTL*GSRSIEKTNGATEQIGRDESGGGGG-SDPGEAPTRAARGELRSTQGPLSSAPE

Parental  IVHEDLKMGSDGESDQASATSSDEVQSPVRVRMRNHPPRKISTEDINKRLSLPADIRLPEGYLEKLTLNS
          IVHEDLKMGSDGESDQASAT.SDEVQSPVRV.M.NHPP.KISTEDINK.LSLPAD..LPE.YLEKLTLNS
Retrocopy IVHEDLKMGSDGESDQASATFSDEVQSPVRVPMHNHPPCKISTEDINKHLSLPADTWLPESYLEKLTLNS

Parental  PIFDKPLSRRLRRVSLSEIGFGKLETYIKLDKL-GEGTYATVYKGKSKLTDNLVALKEIRLEHEEGAPCT
          PIFDK.LSRRL..VSLSE.GFGKLETYIKLD...G.G.Y........KLTDNLV.LKE.RLEH.EG.PCT
Retrocopy PIFDKSLSRRLHHVSLSETGFGKLETYIKLDNV<GRG-YLCHRLQRQKLTDNLVVLKETRLEHGEGTPCT

Parental  AIREVSLLKDLKHANIVTLHDIIHTEKSLTLVFEYLDKDLKQYLDDCGNIINMHNVKLFLFQLLRGLPYC
          AIREVSLLKDLKHANIV...DIIH.EKSL.LVFEYLDKDLKQYLDDCGNIINMHN.KLFLFQLL.GL.YC
Retrocopy AIREVSLLKDLKHANIVMVRDIIHLEKSLSLVFEYLDKDLKQYLDDCGNIINMHNMKLFLFQLLHGLAYC

Parental  HRQKVLHRDLKPQNLLINERGELKLADFGLARAKSIPTKTYSNEVVTLWYRP-PDILLGSTDYSTQIDMW
          H.QKVLH.DLKPQNLLINERGELKLADFGLARAKSIPTK.YSNEV.TLWY.P.PDILLGSTDYSTQIDMW
Retrocopy HQQKVLH*DLKPQNLLINERGELKLADFGLARAKSIPTKMYSNEVGTLWYCP<PDILLGSTDYSTQIDMW

Parental  GVGCIFYEMATGRPLFPGSTVEEQLHFIFRILGTPTEETWPGILSNEEFKTYNYPKYRAEALLSHAPRLD
          .VGCIFYEMATG..LFPGS.VEEQLHFIF.ILGTPTEETWPGILSN..FKTYNYPKY.AEA.LSH.PRLD
Retrocopy RVGCIFYEMATGWALFPGSMVEEQLHFIFHILGTPTEETWPGILSNKKFKTYNYPKYQAEAFLSHTPRLD

Parental  SDGADLLTKLLQFEGRNRISAEDAMKHPFFLSLGERIHKLPDTTSIFALKEIQLQKEASLRSSSMPDSGR
          SDG.DLLTKLLQFEGRNRISAEDAMKHPFFL.LGERIHKLPDT.SIFALKEIQLQKE.SLRSSSMPDSGR
Retrocopy SDGTDLLTKLLQFEGRNRISAEDAMKHPFFLGLGERIHKLPDTSSIFALKEIQLQKEDSLRSSSMPDSGR

Parental  PA-FRVVDTEF
          PA.FRVVDTEF
Retrocopy PA>FRVVDTEF

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	0.51 RPM	8.28 RPM
SRP051959_heart	0.44 RPM	13.40 RPM
SRP051959_kidney	0.67 RPM	10.32 RPM
SRP051959_liver	0.58 RPM	4.07 RPM
SRP051959_lung	0.55 RPM	8.28 RPM
SRP051959_lymph_node	0.73 RPM	7.81 RPM
SRP051959_skeletal_muscle	0.35 RPM	18.96 RPM
SRP051959_spleen	0.65 RPM	7.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_961 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_961 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Callithrix jacchus	ENSCJAG00000007001	2 retrocopies	retro_cjac_1846, retro_cjac_671,
Callithrix jacchus	ENSCJAG00000012261	1 retrocopy	retro_cjac_961 ,
Callithrix jacchus	ENSCJAG00000014175	1 retrocopy	retro_cjac_4070,
Callithrix jacchus	ENSCJAG00000020258	1 retrocopy	retro_cjac_1522,
Dipodomys ordii	ENSDORG00000002798	1 retrocopy	retro_dord_501,
Echinops telfairi	ENSETEG00000003242	1 retrocopy	retro_etel_2002,
Myotis lucifugus	ENSMLUG00000013128	1 retrocopy	retro_mluc_209,