RetrogeneDB ID: retro_cjac_4201

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:89407940..89409311(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTDSPL2
• Ensembl ID: ENSCJAG00000002423
• Aliases: None
• Description: None

Sequence

>retro_cjac_4201
AGATTGAGAACGTGGGAAGCTTCTCAGCAGTCAAATCAAATCCAAACACAACTCACTGCCAGAGCAAAGAGGAAATATTC
AGAGGCTGATGAAACCTACTTTTAGGAGGAGAGAAACCACTAAAGAATGAAACTGGCTTGTCTTCAATTAAAAAACCATT
AAAGGAAGCACACGTAAGGAAGAGAGAGAAAATCCTTTAAAATGGAGTAGAATCGAACTTGATATAGATAGCAATTTGAT
CACATCAACACCAAGAGCAGGAGAGAAATCTAACAAACAGATACCTTGAGTAAGACAGAAAAGTCAAGTAAATGGAGAAG
CTGGTAGTTATCAAAAGACAAATCAATTTATAAAATAAAATGGAAAATTAGAAAATAATCCTTCCTCTGGCAGTTCTCCA
AGGACTACTTTGTAGGGGACCATATTTTCTCTGGTCTTCAACTTTTTTCATCAACAAATAAAAATGGAACATCAGGATCA
GATTCTCCAGGACACACTGTGGAAGCTGAAGAAATGGTAAAATAACTTGATATGGGACAGGTGGATGAGATCACTATCAG
TACTACTACATCAACTAATGGAGCAACTAATGCAAATCAAGCAGTTCAGGTGAAACCATCAATAAACAATAGTTTAGAGG
AAACAGTAATCATGATATCTCACCCCTTACAGCACCAGTAATTCCAGATAGTAGTTATTCATCATCCCATACAGACGCCA
CCTATGAAGAAGGCTGGGAAGTATTTTGCCCCTATTATTTCATCAAACATGTCTCGCCACTGACAGAAGAACAACTAAAT
AGGAAACCTCTTTTGTTGAAAACAGGAAGTACACAGGAATTCTCCCTAGATTTAGATTTGGATGAAACACTAAGTGCACT
GTAGTCTAAATGAGCTAGAAGATGCAGCACTTAATTTTCCAGTCATTTTCCATGATGTCATTTATCAGGTTTATGAGATT
AAGATCATTTTTCAGGGAATTCCTGGAGTAATTTTTCAGATGGATGAGATTATTCTTTTTCCTGCTTTTAAGAAGGTGTA
TGCAGACAAGTTACTGACCAAACTAGACCCTAAAAAGCAAAGGGTCAAGTCCAATTTTTCTGTGATCATTGTGTTTGTAC
AAGGAAAATATATAAAGGACTTAAATATTATTGGAAGAGATCTTTCAAAAACTATAATAATTGACAACTCACCACAAGAC
TTTGCATATTCGCTTTCTAATGGAATCCCTATAGAAAGTTGGTTTATGAATAAAAATGACAATGAACTTCTAAAATTGCT
TTTATTCCTGGAGAAGCTTGTATAACTGAGTGAAGATGTTTGACCACACATCAGACACAGATTTCACTAGCATGATTTGC
TGACCCATGAT

Alignment

ORF - retro_cjac_4201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 99.79 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RLRTRKASQQSNQIQTQRTARAKRKYSEVDDS-LPSGGEKPRKNETGLLSSIKK-FIKGSTPKEERENPS
          RLRT..ASQQSNQIQTQ.TARAKRKYSE.D...L..GGEKP.KNETGL.SSIKK..IKGST.KEERENP.
Retrocopy RLRTWEASQQSNQIQTQLTARAKRKYSEADET<LLLGGEKPLKNETGL-SSIKK<TIKGSTRKEERENPL

Parental  KRSRIERDIDNNLITSTPRAGEKPNKQISRVRRKSQVNGEAGSYEMTNQHVKQNGKLEDNPSAGSPPRTT
          K.SRIE.DID.NLITSTPRAGEK.NKQI..VR.KSQVNGEAGSY..TNQ..K.NGKLE.NPS.GS.PRTT
Retrocopy KWSRIELDIDSNLITSTPRAGEKSNKQIP*VRQKSQVNGEAGSYQKTNQFIK*NGKLENNPSSGSSPRTT

Parental  LLGTIFSPVFNFF-SPANKNGTSGSDSPGQAVEAEEIVKQLDMEQVDEITTSTTTSTNGAAYSNQAVQVR
          L.GTIFS.VFNFF.S..NKNGTSGSDSPG..VEAEE.VK.LDM.QVDEIT.STTTSTNGA...NQAVQV.
Retrocopy L*GTIFSLVFNFF<SSTNKNGTSGSDSPGHTVEAEEMVK*LDMGQVDEITISTTTSTNGATNANQAVQVK

Parental  ASINNGLEEAEETV-NRDIPPLTAPVTPDSGYSSAHAEATYEEDWEVFDPYYFIKHVPPLTEEQLNRKPA
          .SINN.L...EETV.N.DI.PLTAPV.PDS.YSS.H..ATYEE.WEVF.PYYFIKHV.PLTEEQLNRKP.
Retrocopy PSINNSL---EETV<NHDISPLTAPVIPDSSYSSSHTDATYEEGWEVFCPYYFIKHVSPLTEEQLNRKPL

Parental  LPLKTRSTPEFSLVLDLDETL-VHCSLNELEDAALTFPVLFQDVIYQVYVRLRPFFREFLERMSQMYEII
          L.LKT.ST.EFSL.LDLDETL.VHCSLNELEDAAL.FPV.F.DVIYQVY......F........QM.EII
Retrocopy L-LKTGSTQEFSLDLDLDETL>VHCSLNELEDAALNFPVIFHDVIYQVY-EIKIIFQGIPGVIFQMDEII

Parental  LFTASKKVYADKLLNILDPKKQLVRH-RLFREHCVCVQGNYIKDL-NILGRDLSKTIIIDNSPQAFAYQL
          LF.A.KKVYADKLL..LDPKKQ.V.....F..HCVC....Y.K.L.NI.GRDLSKTIIIDNSPQ.FAY.L
Retrocopy LFPAFKKVYADKLLTKLDPKKQRVKS<QFFCDHCVCTRKIY-KGL>NIIGRDLSKTIIIDNSPQDFAYSL

Parental  SNGIPIESWFMDKNDNELLKLIPFLEKLVELNEDVRPHIRDRFRLHDLLPPD
          SNGIPIESWFM.KNDNELLKL..FLEKLV.L.EDV.PHIR.RF..HDLL..D
Retrocopy SNGIPIESWFMNKNDNELLKLLLFLEKLV*LSEDV*PHIRHRFH*HDLLTHD

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	26.40 RPM
SRP051959_heart	0.00 RPM	23.66 RPM
SRP051959_kidney	0.00 RPM	28.84 RPM
SRP051959_liver	0.00 RPM	17.35 RPM
SRP051959_lung	0.00 RPM	37.77 RPM
SRP051959_lymph_node	0.00 RPM	41.30 RPM
SRP051959_skeletal_muscle	0.00 RPM	14.19 RPM
SRP051959_spleen	0.00 RPM	38.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4201 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4201 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4201 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002423	1 retrocopy	retro_cjac_4201 ,
Callithrix jacchus	ENSCJAG00000006503	2 retrocopies	retro_cjac_3087, retro_cjac_919,
Homo sapiens	ENSG00000137770	1 retrocopy	retro_hsap_4881,
Macaca mulatta	ENSMMUG00000016742	1 retrocopy	retro_mmul_2621,