RetrogeneDB ID: retro_cjac_2152

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:78915638..78916680(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIR1
• Ensembl ID: ENSCJAG00000007884
• Aliases: None
• Description: corepressor interacting with RBPJ, 1 [Source:HGNC Symbol;Acc:24217]

Sequence

>retro_cjac_2152
AAAGAGAAAGAAGAAACAGAGGAAAGACTGAATACAAATTTGAATGGCAGGAAGGAGCTCCACAAGAAAAATATGCCGAG
GATGACGTGAACATCAGAGATCAGCCCTTTGGTATTCAAGTTCGAAATTTGAGGTGCATTAAATGTCACAAATGGGGTCA
CATAAACACAGGTGGAGAATATCCTCTGTTTGGTCTTTCTGGAATCAATGCAAGTTCAGTTCCTAGTGATGGCTCAGGGC
CATCAATGCATCCTTCAGGGCCAATAGAGGAAACAAGAAACACTGGATTTTCTCTCCAGTGAAATGTACGGTAGAGAAAC
GTGACCACAAATAATCCATCACAGGAGTATGTTGTAAGTGAGGGTGAAGAAGATCCAGTAGTTCAATTTTTAAAGTCATT
AATGACCAAACAAAAAAGAAACTTCTCAGGAAGGTAGATAAACCGGAGAAGAAAAAAAGAAAAAGAAAAGAGATAGAAAA
AAGAAAAAGTTTCAGAAGAGCAGAAGTACACACAAAAAGCATAAAAACAAATCCTCTTCCTCCTCCTCCTCCTCTTCCCC
TACTGAAAGCAATAGTGAGAGTGGGAGTAACATTCAATTAAAAAAAAAAAGAAAAGAAGAAAACAAAGTAAAACAAGAGC
TTAGGACATAAAACAGTGATTCTAAAGAGAAGGGCAAGTCTAAAAAGACAAAACACTTTATGAAAACTTTTCTAGCAGTC
ACCCTAACCAGGAAAATGCTAAGGAAAGGCTTGAGTTCTTAAAACATGAGAGTTCTAGGGAGATAGCAAACAGAGCCATT
CAGATTCTAACAAAAAGTCTGGAAGCCATAATCATAGCCCAAAGAAGAGAGCGTCTGGAAGAAAAGAGGGGAGCATCAGA
AGCTGTGGCAGGGATGAAAGGAGCAGGAGAAGCCGAAGCACAAGTCCTGGTAGCTATAAGCAAAGGGAAATAAGAAAACA
GCCACAGCGAGGTCCCAGTGGAAAGTGTAGTAGAATAAATGACAACAGAAGCTGTGGCATAGATGTTTACAGAGAAGAAA
AA

Alignment

ORF - retro_cjac_2152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.69 %
• Parental protein coverage: 78.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KEKEETE-GETEYKFEWQKGAPREKYAKDDMNIRDQPFGIQVRNVRCIKCHKWGHVNTDRECPLFGLSGI
          KEKEETE.G.TEYKFEWQ.GAP.EKYA.DD.NIRDQPFGIQVRN.RCIKCHKWGH.NT..E.PLFGLSGI
Retrocopy KEKEETE<GKTEYKFEWQEGAPQEKYAEDDVNIRDQPFGIQVRNLRCIKCHKWGHINTGGEYPLFGLSGI

Parental  NASSVATDGSGPSMHPSELIAEMRNSGFALKRNVLGRNLTANDPSQEYVASEGEEDPEVEFLKSLTTKQK
          NASSV..DGSGPSMHPS..I.E.RN.GF.L..NV..RN.T.N.PSQEYV.SEGEEDP.V.FLKSL.TKQK
Retrocopy NASSVPSDGSGPSMHPSGPIEETRNTGFSLQ*NVR*RNVTTNNPSQEYVVSEGEEDPVVQFLKSLMTKQK

Parental  Q-KLLRKLDRLEKKK-KKKDR-KKKKKLQKSRS---KHKKHKSSSSSSTETSESSSESESD---NKEKKI
          ..KLLRK.D..EKKK.KKK.R..KKKK.QKSRS...KHK.............ES.SES.S.....K..K.
Retrocopy R<KLLRKVDKPEKKK<KKKKRDRKKKKFQKSRSTHKKHKNKXXXXXXXXXPTESNSESGSNIQLKKKRKE

Parental  ERKKRKKSKCSVQNSSDSEEKSKKR-TLHEELSSSHHNKEKAKEKPRFLKHESCRE-NSKRSHSNSDKKS
          E.K...........S.......K...TL.E..SSSH.N.E.AKE...FLKHES.RE..SK.SHS.S.KKS
Retrocopy ENKVKQELRT*NSDSKEKGKSKKTK<TLYENFSSSHPNQENAKERLEFLKHESSRE<DSKQSHSDSNKKS

Parental  RSCNHSPEKRGSERNEGSGRSHGRDERSRRSRSRSPGSYKQRELRKWPQRSPTEEQSRRNDTRSHGVDVY
          .S.NHSP.KR.S.R.EGS.RS.GRDERSRRSRS.SPGSYKQRE.RK.PQR.P....SR.ND.RS.G.DVY
Retrocopy GSHNHSPKKRASGRKEGSIRSCGRDERSRRSRSTSPGSYKQREIRKQPQRGPSGKCSRINDNRSCGIDVY

Parental  RGGK
          R..K
Retrocopy REEK

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	28.13 RPM
SRP051959_kidney	0.00 RPM	26.87 RPM
SRP051959_liver	0.00 RPM	27.21 RPM
SRP051959_lung	0.02 RPM	29.30 RPM
SRP051959_lymph_node	0.00 RPM	22.10 RPM
SRP051959_skeletal_muscle	0.00 RPM	30.88 RPM
SRP051959_spleen	0.00 RPM	25.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2152 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2152 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007884	1 retrocopy	retro_cjac_2152 ,
Homo sapiens	ENSG00000138433	2 retrocopies	retro_hsap_3082, retro_hsap_3394,
Macaca mulatta	ENSMMUG00000023006	1 retrocopy	retro_mmul_1967,
Mustela putorius furo	ENSMPUG00000013943	1 retrocopy	retro_mputfur_178,
Mus musculus	ENSMUSG00000041777	2 retrocopies	retro_mmus_2064, retro_mmus_3104,
Nomascus leucogenys	ENSNLEG00000005869	3 retrocopies	retro_nleu_1540, retro_nleu_2013, retro_nleu_2691,
Pan troglodytes	ENSPTRG00000012652	2 retrocopies	retro_ptro_2079, retro_ptro_2306,