RetrogeneDB ID: retro_cjac_2617

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:63525825..63527488(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIOK3
• Ensembl ID: ENSCJAG00000020556
• Aliases: None
• Description: RIO kinase 3 [Source:HGNC Symbol;Acc:11451]

Sequence

>retro_cjac_2617
TTGCTCTGGCACTAGCAGCCAGTCGCCCCTGCCCTGCCCATCTCCGAGGCAGAGCCTACTTCCTGTCCTGCCACCTCTCT
GCTCTGTTTTTGTCGCTGCCTTCATCCCCCAATGGATCTGGTAGGAGTGGCATCGCCTGAGCCCGGGCCAGCAGCGGCCT
GGGGACCCAGCAAGTGTCCGTGGGCTATCGCTCAAAATACAATATCTAGTTCTTTGGCTGAGGTAATGAGTGAACAGCTG
GCCAAAGAATTGCAGTTAGAAGAAGCAGCTGCTGTTTTTCCTGAAGTTGCTGTTGCCGAAGGACCATTTATTACTGGATA
AAACATTGATACTTCCAGTGACCTTATGCTGGCTCAGATACTATTGATGGACTTTGACAGAGAATATGATGCACAGCTTA
GGTGTGAAGAAAAAACATTCAATGGAGATAGCAAAGTTTCCATTTCCTTTGAGAATTATCGAGAAGTGCATCCTTATGAA
GACAGCGATAGCTCTGAAGATGAGGCTGACTGGCAGGTACTCAGGATGATCCATCCCTACAGACCAGCAAAACCGGCTCC
CACTCCTAAAAAGGGTTTTATTGGAAAAGGAAAAGATATCACCACCAAACATGATGAAGTAGTATGTGGGAGAAAGAATA
CAGCAGGAATGGAAAATTTTGCACCTGAGTTTCAGGTAGGGGATGAATTGAAATGGACTTAAAACTATCAAACCATGTTT
CCGATGCTTTATAACAACATGCCTACTCAGAAGAATGTCAAAGTGCCCAGCTACATGAAAAAAAGGAGCATTCAACAGCA
GAAAAAGCAGTTGATCCTAAGACACGTTTGCTTATGTATAAAATGGTGAACTCTGGAATGCTGGAGACAATCACTGGCTG
TATTAATACAGGAAAGGAATCTGTTGTCTTTCATGCATATGGAGGGAGCACGGAGGATGAAAAGGAAGACAGTAAAGTTA
TACCTACAGAATGTGCCCTCAAGGTATTTAAAACAACACTTAATGAGTTTAAGAATCGTGACAAATATATTAAGGATGAT
TTCAGGTTTAAAGATTGCTTCAGCAAACTACATCCATGTAAGATCATCTGCATGTGGGCAGAAAAAGAAAGGCACAATCT
CACAAGAATGCAGACAGCTGAAATTTCTTGTCCAACAATTGTACTACTCAAGAAACACATTTTTCTTATGTCTTTTGTTG
GCCATGATCAAGTTCCAGCTTCTAAATTAAAAGAAGTAAAGCTCAATAGTGAAGAAATGAAAGAAGCCTACTATCAAACT
CTTCATCTGATGCAGCAGTTATATAACGAATATACACTCATCCACGCTGACCTCAGTGAATACAACATGCTGTGGCATGC
TAGAAAGGTCTGGTTGATTGATGTCAGTCAGTCAGTAGAACCTACCCATCCTCATGGCCTGGAGCTCTTGTTCCAGGACT
CAGGAATGTCTCGCAGTTTTTCCAGAAAGGAGGAGTCAAGGAAGCCCTTAGTGAACTCTTCAATGCTGTTTCAGGCTTAA
ACATCTCAGCAGATAATGAATCTGATTTTTTAGCTGAGATAGAAGCTTTGGAGAAAATGAATGAAGATCACATTCAGAAG
AATGGAAGGAAAGCTGCTTCATTTTTGAAAGATGATGGAGACCCACCAGGACCATATGATGAA

Alignment

ORF - retro_cjac_2617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.55 %
• Parental protein coverage: 90.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLRHQQPVAPAPPVSSAEPASRPATSLLCFCRCLHPPMDLVGVASPEPGPAAAWGPSKCPWAIPQNTISC
          LL.H.QPVAPA.P.S.AEP.S.PATSLLCFCRCLHPPMDLVGVASPEPGPAAAWGPSKCPWAI.QNTIS.
Retrocopy LLWH*QPVAPALPISEAEPTSCPATSLLCFCRCLHPPMDLVGVASPEPGPAAAWGPSKCPWAIAQNTISS

Parental  SLADVMSEQLAKELQLEEEAAVFPEVAVAEGPFITGENIDTSSDLMLAQMLQMEFDREYDAQLRREEKKF
          SLA.VMSEQLAKELQLEE.AAVFPEVAVAEGPFITG.NIDTSSDLMLAQ.L.M.FDREYDAQLR.EEK.F
Retrocopy SLAEVMSEQLAKELQLEEAAAVFPEVAVAEGPFITG*NIDTSSDLMLAQILLMDFDREYDAQLRCEEKTF

Parental  NGDSKVSISFENYRKVHPYEDSDSSEDEVDWQDTRD-DPYRPAKPVPTPKKGFIGKGKDITTKHDEVVCG
          NGDSKVSISFENYR.VHPYEDSDSSEDE.DWQ..R...PYRPAKP.PTPKKGFIGKGKDITTKHDEVVCG
Retrocopy NGDSKVSISFENYREVHPYEDSDSSEDEADWQVLRMIHPYRPAKPAPTPKKGFIGKGKDITTKHDEVVCG

Parental  RKNTARMENFAPEFQVGDG-IGMDLKLSNHVFNALKQHAYSEERRSARLHEKKEHSTAEKAVDPKTRLLM
          RKNTA.MENFAPEFQVGD..I.MDLKLSNHV..AL.QHAYSEE..SA.LHEKKEHSTAEKAVDPKTRLLM
Retrocopy RKNTAGMENFAPEFQVGDE<IEMDLKLSNHVSDAL*QHAYSEECQSAQLHEKKEHSTAEKAVDPKTRLLM

Parental  YKMVNSGMLETITGCISTGKESVVFHAYGGSMEDEKEDSKVIPTECAIKVFKTTLNEFKNRDKYIKDDFR
          YKMVNSGMLETITGCI.TGKESVVFHAYGGS.EDEKEDSKVIPTECA.KVFKTTLNEFKNRDKYIKDDFR
Retrocopy YKMVNSGMLETITGCINTGKESVVFHAYGGSTEDEKEDSKVIPTECALKVFKTTLNEFKNRDKYIKDDFR

Parental  FKDRFSKLNPRKIIRMWAEKEMHNLTRMQRAGIPCPTVVLLKKHILVMSFIGHDQVPAPKLKEVKLNSEE
          FKD.FSKL.P.KII.MWAEKE.HNLTRMQ.A.I.CPT.VLLKKHI..MSF.GHDQVPA.KLKEVKLNSEE
Retrocopy FKDCFSKLHPCKIICMWAEKERHNLTRMQTAEISCPTIVLLKKHIFLMSFVGHDQVPASKLKEVKLNSEE

Parental  MKEAYYQTLHLMRQLYNECTLVHADLSEYNMLWHAGKVWLIDVSQSVEPTHPHGLEFLFRD-CRNVSQFF
          MKEAYYQTLHLM.QLYNE.TL.HADLSEYNMLWHA.KVWLIDVSQSVEPTHPHGLE.LF.D..RNVSQFF
Retrocopy MKEAYYQTLHLMQQLYNEYTLIHADLSEYNMLWHARKVWLIDVSQSVEPTHPHGLELLFQD<LRNVSQFF

Parental  QKGGVKEALSERELFNAVSGLNISADNEADFLAEIEALEKMNEDHVQKNGRKAASFLKDDGDPPVPYDE
          QKGGVKEALS..ELFNAVSGLNISADNE.DFLAEIEALEKMNEDH.QKNGRKAASFLKDDGDPP.PYDE
Retrocopy QKGGVKEALS--ELFNAVSGLNISADNESDFLAEIEALEKMNEDHIQKNGRKAASFLKDDGDPPGPYDE

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	0.04 RPM	35.90 RPM
SRP051959_heart	0.61 RPM	23.47 RPM
SRP051959_kidney	0.13 RPM	29.60 RPM
SRP051959_liver	0.04 RPM	33.14 RPM
SRP051959_lung	0.86 RPM	42.44 RPM
SRP051959_lymph_node	0.07 RPM	31.12 RPM
SRP051959_skeletal_muscle	0.07 RPM	48.02 RPM
SRP051959_spleen	0.02 RPM	40.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2617 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2617 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008343	1 retrocopy	retro_chof_1788,
Callithrix jacchus	ENSCJAG00000020556	1 retrocopy	retro_cjac_2617 ,
Echinops telfairi	ENSETEG00000003689	1 retrocopy	retro_etel_2181,
Macropus eugenii	ENSMEUG00000006292	1 retrocopy	retro_meug_1278,
Macaca mulatta	ENSMMUG00000021478	1 retrocopy	retro_mmul_1291,
Ochotona princeps	ENSOPRG00000004803	2 retrocopies	retro_opri_1034, retro_opri_946,
Pongo abelii	ENSPPYG00000009062	1 retrocopy	retro_pabe_1011,