RetrogeneDB ID: retro_cjac_3887

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285848.1:8867..10057(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUBP3
• Ensembl ID: ENSCJAG00000020542
• Aliases: None
• Description: far upstream element (FUSE) binding protein 3 [Source:HGNC Symbol;Acc:4005]

Sequence

>retro_cjac_3887
GGGGCCATGGTACATCAAAGGACCGTAATAAGGGAAGAATTCAAAGTGCCTGACGAAATGGTTGGATTTATTATCGGCAG
GGGAGGTGAGCAGATTTCACGGATTCAAGCAGAATCTGGTTGCAAAATTCAGATTGCTTCAGAGAGTTCTGGGATTCCAG
AGAGGCCCTGGGTACTTACTGGAACCACAGAAATTATTGAACACGCCAAACAACTCCTGGGGCAGATTGCGGACCGCTGT
CTAAATGGACCTGGCTTTCATCATGACATAGACAGCAACAGCACAATCCAGGAGATTCTCATTCCCGCATCTAAAGTGGG
TCTTGTCATCGGCAGAGGACGGGAAACAATCAAGCAGTTGCAGGAGCCGAAAGGCGTGAAGATGGTTATGATCCAGGACG
GCCCATTGCCCACGGGAGCAGACAAGGCTCTTCGTATCACTGGAGACCCATTTAAAGTACAACAAGCAAGAGAAATGGTA
CTAGAGATTTTCCGAGAAAAAGACCAAGCTGACTTTCGGGGTGTACACTCCCGGGGTGATTTCAGCTCCCGAATGGGAGG
AGGCAGTATTGAGGTATCTGTGCCTAGATTCGCTGTGGGGATTGTAATAGGAAGAAACGGGGAAATGATCAAAAAGATCC
AGAGTGATGCTGGTGTGAGGATTCAGTTTAAACCAGACGATGGGATTAGTCCAGAAAGAGCTGCGCAGGTCATGGGCCCT
CCGGATCGGTGTCAGCATGCAGTGCACATCATCAACGAGCTGATTCTTACAGCCCAGGAAAGAGACGGCTTTGGAGGCCT
GGCAGTAGCCAGAGGAAGAGGTCGTGGCCGTGGCGACTGCAGTGTGGGAGCCCCTGGTGGCGTCCAGGAGATAACATACA
TGGTGCCAGCCCATAAATGTGGCCTTGTCATAGGCAAAGGGGGTGAGAACATCAAAAGCATCAACCAGCAGTCAGGGGCG
CATGTGGAGCTCCAGAGGAACCCCCCTCCCAACTGGACCCTAACCTGCGGAGATTCACCATCAAGGGGATTCCCCAGCAG
ATCGAGGTGGCCAGGCAGCTCACAGATGAGAAAGTTGGTGGGACCAGTCTTGGAGCACCTGGAGCCTTCGGACAGAGTCC
CTTCAGCCAGCCACCTGCCCTACATCATCAAAACGCCTTTCCTCCAAGGAGCTCTGGGTGCTTCCCCCAC

Alignment

ORF - retro_cjac_3887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.96 %
• Parental protein coverage: 69.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GALVHQRTVITEEFKVPDKMVGFIIGRGGEQISRIQAESGCKIQIASESSGIPERPCVLTGTPESIEQAK
          GA.VHQRTVI.EEFKVPD.MVGFIIGRGGEQISRIQAESGCKIQIASESSGIPERP.VLTGT.E.IE.AK
Retrocopy GAMVHQRTVIREEFKVPDEMVGFIIGRGGEQISRIQAESGCKIQIASESSGIPERPWVLTGTTEIIEHAK

Parental  RLLGQIVDRCRNGPGFHNDIDSNSTIQEILIPASKVGLVIGRGGETIKQLQERTGVKMVMIQDGPLPTGA
          .LLGQI.DRC.NGPGFH.DIDSNSTIQEILIPASKVGLVIGRG.ETIKQLQE..GVKMVMIQDGPLPTGA
Retrocopy QLLGQIADRCLNGPGFHHDIDSNSTIQEILIPASKVGLVIGRGRETIKQLQEPKGVKMVMIQDGPLPTGA

Parental  DKPLRITGDPFKVQQAREMVLEIIREKDQADFRGV--RGDFSSRMGGGSIEVSVPRFAVGIVIGRNGEMI
          DK.LRITGDPFKVQQAREMVLEI.REKDQADFRGV..RGDFSSRMGGGSIEVSVPRFAVGIVIGRNGEMI
Retrocopy DKALRITGDPFKVQQAREMVLEIFREKDQADFRGVHSRGDFSSRMGGGSIEVSVPRFAVGIVIGRNGEMI

Parental  KKIQNDAGVRIQFKPDDGISPERAAQVMGPPDRCQHAAHIINELILTAQERDGFGGLAVARGRGRGRGDW
          KKIQ.DAGVRIQFKPDDGISPERAAQVMGPPDRCQHA.HIINELILTAQERDGFGGLAVARGRGRGRGD.
Retrocopy KKIQSDAGVRIQFKPDDGISPERAAQVMGPPDRCQHAVHIINELILTAQERDGFGGLAVARGRGRGRGDC

Parental  SVGAPGGVQEITYTVPADKCGLVIGKGGENIKSINQQSGAHVELQRNPPPN-SDPNLRRFTIRGVPQQIE
          SVGAPGGVQEITY.VPA.KCGLVIGKGGENIKSINQQSGAHVELQRNPPPN..DPNLRRFTI.G.PQQIE
Retrocopy SVGAPGGVQEITYMVPAHKCGLVIGKGGENIKSINQQSGAHVELQRNPPPN<LDPNLRRFTIKGIPQQIE

Parental  VARQLIDEKVGGTSLGAPGAFGQSPFSQPPAPPHQNTFPPRSSGCFPN
          VARQL.DEKVGGTSLGAPGAFGQSPFSQPPA..HQN.FPPRSSGCFP.
Retrocopy VARQLTDEKVGGTSLGAPGAFGQSPFSQPPALHHQNAFPPRSSGCFPH

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	19.97 RPM
SRP051959_heart	0.04 RPM	14.54 RPM
SRP051959_kidney	0.02 RPM	22.56 RPM
SRP051959_liver	0.09 RPM	31.34 RPM
SRP051959_lung	0.13 RPM	23.33 RPM
SRP051959_lymph_node	0.05 RPM	17.99 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.40 RPM
SRP051959_spleen	0.04 RPM	20.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3887 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3887 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016627	1 retrocopy	retro_cjac_460,
Callithrix jacchus	ENSCJAG00000020542	1 retrocopy	retro_cjac_3887 ,
Microcebus murinus	ENSMICG00000015452	1 retrocopy	retro_mmur_860,