RetrogeneDB ID: retro_cjac_1271

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:36468914..36470242(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLPB
• Ensembl ID: ENSCJAG00000015121
• Aliases: None
• Description: None

Sequence

>retro_cjac_1271
GGGTGGCACCAGGGAGGATGCTTTGATACCAAATGCCTTATAGCTGCCACTTGGAGACACCTTCCTGGCCCTGAATAAAC
ACTCCCAGGACAGGAAAGCTGGAACAGGGTCCCCGACAGGGCCAGACTGGGCATGTGGGCCCTGACCACAGTGCTGGTGG
TTCATTGCTATAGCAAGAGTCAGTTTAATAAGGATGCAGCCCTGATGGAAGCTGCGTGTGCCAACAATCTGCAAGAAGTC
AGTAGGCTGTTGTCAGAAGGTGCAGATATTAATGCAAGGCACAGACTTGGCTGGACAGCACTCATGGTGGCAGCCATCAA
CCAAAACAACAGTCTGGTACAGGTCCTGCATGCTGCCAGGGCTGATCCAAACCTGGAGATGATTTCAGCAGTGTTTATAA
GACCTCCAAGAAACAGGGAATCCATTCTTTGGAAGTCCTGGTCACCCGAGAGGATGACTTAAACAACTGGCTGAACAACT
GTACCAGTTTCAAGGGCTGCACAGCCCTGCACTATGCTGTGCTTGCTGATGACTGCCGCACTGCCGAGGAGCTGCTCGAT
GGAGGAGCCAACCCCCTGCAGAGTGGTGAAATGGAACACACACCCTTGGATTATACCCAAGAAGGGGAAGTGACAAAGCT
TCTGAGCACTTCTGAAGCCAAGTACCAAGAGAAGCAGCGGAAGCGTGAGGCTGAGAAGTGGTGCTGCTTCCCCTTGGAGC
AGCGACTGAAGGAGCACGTCACTGGCCGGGAGAGTGCTATTGCCGCAGTTGGTGTTGCGATCCAGAGGAAGGAGAATGGT
TGGTACGAGGAAGAACACCCTCTTGGTCTTCCTCTTCTAGGGATCATCTGAAATAGGAAAAACAGAGCTGGTCAAGCAGA
CAGCCAAATATATGCACAAAGATGCTAAAAATGGCTTCATCAGGCTGGACATGTCTGAGTTCCAGGAGCAACACTAGGTG
TCCAAGTTTATCGGGTCCCACCAGGCTACATCAGCCATGAGGAGTGTGGCCAGCTGACCAAGAAGTTGATGCAGTGCCCC
AATGGCATGCTGCTCTTTGATGAAGTAGACAAGGCCCATCCAGATGTGCTCACCATCATGCTGCAGCTGTTGGGTGAGGG
CTGACTGACAGATGGAAAAGGGAAAACCATTGATTGTAAGGACGACATCTTCATCATGACCTCCTGTGTGGCCAGTGACA
ATATCACATAGCATGCGCTGCAGCTGAGGCAGGAAGCTTTGGAGATGAGCTGTAACCGTATTGCTGAAAACCTGGGGGAT
GTCCAGGTAAGTGACAAGATCACCATCTCAAAGAACTTCAAGGAGAAT

Alignment

ORF - retro_cjac_1271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.17 %
• Parental protein coverage: 65.44 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGRHGGRFDTKCLAAAIWGRLPGPEETLPGQDSWTEVPNRAGLGMWVLATALVVHCYSKSPSNKDAALME
          G...GG.FDTKCL.AA.W..LPGPE.TLPGQ.SW..VP.RA.LGMW.L.T.LVVHCYSKS..NKDAALME
Retrocopy GWHQGGCFDTKCLIAATWRHLPGPE*TLPGQESWNRVPDRARLGMWALTTVLVVHCYSKSQFNKDAALME

Parental  AARANNPQEVSRLLSEGADVNARHRLGWTALMVAAINRNYSVIQVLLAAGADPNL-GDDFSSIYKTAKEQ
          AA.ANN.QEVSRLLSEGAD.NARHRLGWTALMVAAIN.N.S..QVL.AA.ADPNL.GDDFSS.YKT.K.Q
Retrocopy AACANNLQEVSRLLSEGADINARHRLGWTALMVAAINQNNSLVQVLHAARADPNL<GDDFSSVYKTSKKQ

Parental  GIHSLEVLVTREDDFNNRLNNRASFKGCTALHYAVLADDYRTVKELLDGGANPLQRNEMGHTPLDYAREG
          GIHSLEVLVTREDD.NN.LNN..SFKGCTALHYAVLADD.RT..ELLDGGANPLQ..EM.HTPLDY..EG
Retrocopy GIHSLEVLVTREDDLNNWLNNCTSFKGCTALHYAVLADDCRTAEELLDGGANPLQSGEMEHTPLDYTQEG

Parental  EVMKLLRTSEAKHQEKQRKREAEERRRFPLEQRLKEHIIGQESAIATVGAAIRRKENGWYDEEHP-LVFL
          EV.KLL.TSEAK.QEKQRKREAE....FPLEQRLKEH..G.ESAIA.VG.AI.RKENGWY.EEHP.LVFL
Retrocopy EVTKLLSTSEAKYQEKQRKREAEKWCCFPLEQRLKEHVTGRESAIAAVGVAIQRKENGWYEEEHP>LVFL

Parental  FLGSSGIGKTELAKQTAKYMHKDAKKGFIRLDMSEFQERHEVAKFIGS-PPGYVGHEEGGQLTKKLRQCP
          F.GSS.IGKTEL.KQTAKYMHKDAK.GFIRLDMSEFQE.H.V.KFIGS.PPGY..HEE.GQLTKKL.QCP
Retrocopy F*GSSEIGKTELVKQTAKYMHKDAKNGFIRLDMSEFQEQH*VSKFIGS<PPGYISHEECGQLTKKLMQCP

Parental  NAVVLFDEVDKAHPDVLTIMLQLFDEGRLTDGKGKTIDCKDAIFIMTSNVASDEIAQHALQLRQEALEMS
          N...LFDEVDKAHPDVLTIMLQL..EG.LTDGKGKTIDCKD.IFIMTS.VASD.I..HALQLRQEALEMS
Retrocopy NGMLLFDEVDKAHPDVLTIMLQLLGEG*LTDGKGKTIDCKDDIFIMTSCVASDNIT*HALQLRQEALEMS

Parental  RNRIAENLGDVQISDKITISKNFKEN
          .NRIAENLGDVQ.SDKITISKNFKEN
Retrocopy CNRIAENLGDVQVSDKITISKNFKEN

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	12.89 RPM
SRP051959_heart	0.02 RPM	15.24 RPM
SRP051959_kidney	0.00 RPM	20.99 RPM
SRP051959_liver	0.00 RPM	10.61 RPM
SRP051959_lung	0.02 RPM	9.94 RPM
SRP051959_lymph_node	0.02 RPM	10.46 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.11 RPM
SRP051959_spleen	0.00 RPM	12.63 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1271 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1271 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015121	1 retrocopy	retro_cjac_1271 ,
Mus musculus	ENSMUSG00000001829	1 retrocopy	retro_mmus_3255,