RetrogeneDB ID: retro_cjac_913

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:58057528..58058977(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORC3
• Ensembl ID: ENSCJAG00000000730
• Aliases: ORC3, ORC3L
• Description: None

Sequence

>retro_cjac_913
GAAAGCTTTGCCACAAAATTACTGCAAGACTTCATAATTATCAGCAGTCAACATCTGCATGAATTTCCACTAATACTCAT
TTTTGTAATGCTGCATCTTCTATTATCATCCACTGATTGCTTCCTCATGCAGTATCATCTCTATTGTGCATAGAACCGTT
CCAGGCTTGCAAGGAGCTCCTGACTATGGTACTTGATAAACTACTACTTACAACTCAGTTTCCCTTTAAAATAAATTAAA
AAGTATTACAGGTTCTGCCCAACATCTTTTTGTGTCATGATTTCTCAATTCAAAACTTTATTAAAGGACTTCAGCTTTCT
CTATTTGAGCATTTCTATTCCCAGCCCTTAAGTGTCCTCTACTATAATCTTCCAGAAGCCCAGAAAGAATAAATTTTTTA
TCAAGTAATCAATGTGAAAACATCTGCCCTCTTCCATCTTTTAGGAGGTACATGGAAAAGCAAGCTTCAGAAAAGCAAGT
TGTGCTCTTGACTAATGAGAGATGTTTGAAGGAGGAAACACAATTATTACTAGAAAATCTGCCTGTTTATAATATGAATT
ACTTCCTGACCTTGAGATGTCTTCATAAATTTACCTCTTCTCTTCCCAAGTATCCACTAGGTCGACAGATCAGAGAGTTG
TACTGTACATGTTTAGAAAAGAACATATGGAATTCAGAGGAGTATGCATCAGTCTTGCAGCTGCTGAGGATGTTAGCAAA
GGATGAAATGATGACCATACTTGAGAAATGTTTCAAAGTTTTTAAGTCTTGTTGTGAAAAGCACCTTAGTAGCACAGAGA
AGAGAATAGAGGAGTTCCTGGCCCTGTTTCAGAGCCTCAGTGGAATCAAAGAGGAAGAAGATGATTCTGGGTCACAGCCA
AAGGGGCTTCAGAAGCCAGACCTCTATAATCTTCAGAAGTCCTTACTAGAAATGAAGGAGTTAAGAAGAAGTAAGAAGCG
AACCTGATTTGAAGTACTCAGAGAAAATGTGAACTTCATTGACTGTCTAGTGAGAGAATACCTTCTACCTCCTGAGACAC
AGCCTCTACATAAGGCAGTGTATTTCAGCACTGCCCATGCCCTTCATGAGCATTCAAATGCTGCTCCGCGAATTGCCCTC
CATACTGCATGCAACAATCCTATTATCTAAAGGATGAAGCACTAAAAAGTGAAAAAGATTGCATTCCAAATATTGCCCCA
GATATCTGTGTAGCATGTAAACTGTACCTAGAATGTAGCAGGCTGATCAACCTTGTGGACTGATCAGAATCTTTTACAAC
AGTTGTGATAGCTCCTGAAAGAATGGATGCAAATTCTGCAACCTCAGAAGAAATGAATGAAATTATCCATGCTTGGTTTA
TTAGAGCTGTTTCTGAAATAGAACTTTTAGGATTTATAAAACCTAGGAAGAAGACTGACCATGTGGCAAGGCTAACATGG
GGAGGCTGC

Alignment

ORF - retro_cjac_913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 86.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ESFTTKVLQDFVIISSQHLHEFPLILIFGI-ATSPIIIHRLLPHAVSSLLCIELFQSLPCKEHLTTVLDK
          ESF.TK.LQDF.IISSQHLHEFPLILIF...A.S.IIIH.LLPHAVSSLLCIE.FQ...CKE.LT.VLDK
Retrocopy ESFATKLLQDFIIISSQHLHEFPLILIFVM<AASSIIIH*LLPHAVSSLLCIEPFQA--CKELLTMVLDK

Parental  LLLTTQFPFKINEKVLQVLTNIFLYHDFSIQNFIKGLQLSLLEHFYSQPLSVLCCNLPEAKR-RINFLSN
          LLLTTQFPFKIN.KVLQVL.NIFL.HDFSIQNFIKGLQLSL.EHFYSQPLSVL..NLPEA...RINFLS.
Retrocopy LLLTTQFPFKIN*KVLQVLPNIFLCHDFSIQNFIKGLQLSLFEHFYSQPLSVLYYNLPEAQK<RINFLSS

Parental  NQCENIRRLPSFRRYVEKQASEKQVALLTKEKCLKEETQLLLENLHVYHMNYFLVLRCLHKFTSSLPKYP
          NQCENI..LPSFRRY.EKQASEKQV.LLT.E.CLKEETQLLLENL.VY.MNYFL.LRCLHKFTSSLPKYP
Retrocopy NQCENICPLPSFRRYMEKQASEKQVVLLTNERCLKEETQLLLENLPVYNMNYFLTLRCLHKFTSSLPKYP

Parental  LGRQIRELYCTCLEKNIWDSEEYASVLQLLRMLAKDELMTILEKCFKVFKS-CEKHLGSTAKRIEEFLAQ
          LGRQIRELYCTCLEKNIW.SEEYASVLQLLRMLAKDE.MTILEKCFKVFKS.CEKHL.ST.KRIEEFLA.
Retrocopy LGRQIRELYCTCLEKNIWNSEEYASVLQLLRMLAKDEMMTILEKCFKVFKSCCEKHLSSTEKRIEEFLAL

Parental  FQNLDETKEEEDASGSQPKGLQKTDLYNLQKSLLEMKELRRSKKPTKFEVLRENVVNFIDCLVREYLLPP
          FQ.L...KEEED.SGSQPKGLQK.DLYNLQKSLLEMKELRRSKK.T.FEVLREN.VNFIDCLVREYLLPP
Retrocopy FQSLSGIKEEEDDSGSQPKGLQKPDLYNLQKSLLEMKELRRSKKRT*FEVLREN-VNFIDCLVREYLLPP

Parental  ETQPLHEVVYFSAAHALREHLNAAPRVALHTALNNP-YYYLKNEALKSEEGCIPNIAPDICIAYKLHLEC
          ETQPLH..VYFS.AHAL.EH.NAAPR.ALHTA.NNP.YY.LK.EALKSE..CIPNIAPDIC.A.KL.LEC
Retrocopy ETQPLHKAVYFSTAHALHEHSNAAPRIALHTACNNP<YY-LKDEALKSEKDCIPNIAPDICVACKLYLEC

Parental  SRLINLVDWSEAFATVVTAAEKMDANSATSEEMNEIIHARFIRAVSELELLGFIKPTKQKTDHVARLTWG
          SRLINLVD.SE.F.TVV.A.E.MDANSATSEEMNEIIHA.FIRAVSE.ELLGFIKP.K.KTDHVARLTWG
Retrocopy SRLINLVD*SESFTTVVIAPERMDANSATSEEMNEIIHAWFIRAVSEIELLGFIKPRK-KTDHVARLTWG

Parental  GC
          GC
Retrocopy GC

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	7.48 RPM
SRP051959_heart	0.00 RPM	13.63 RPM
SRP051959_kidney	0.07 RPM	14.09 RPM
SRP051959_liver	0.02 RPM	8.69 RPM
SRP051959_lung	0.00 RPM	12.62 RPM
SRP051959_lymph_node	0.00 RPM	12.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.22 RPM
SRP051959_spleen	0.00 RPM	11.72 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_913 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_913 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_913 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1075

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000730	1 retrocopy	retro_cjac_913 ,
Homo sapiens	ENSG00000135336	1 retrocopy	retro_hsap_798,
Macaca mulatta	ENSMMUG00000002821	1 retrocopy	retro_mmul_1075,
Nomascus leucogenys	ENSNLEG00000012990	1 retrocopy	retro_nleu_413,
Pongo abelii	ENSPPYG00000016830	1 retrocopy	retro_pabe_712,
Pan troglodytes	ENSPTRG00000018408	1 retrocopy	retro_ptro_555,