RetrogeneDB ID: retro_cjac_1830

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:100955142..100956282(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MBD1
• Ensembl ID: ENSCJAG00000004959
• Aliases: None
• Description: None

Sequence

>retro_cjac_1830
GGAGACAGGATCCGAAGCAAGGTAGAGCTGACTCGATACCTGGGCTCTGCGTATCACAGGTAGCTCACCCTCTTCGACGG
CAAACAAGGCATCTTGTGCTATCCAGCTGCCAAGGCCCATTCGTGGCTGTCGCCAGCAAGAAGGGAAAGAAGCCTTCACC
GCCAAGACTCGGAAATGTGAGGTTGGACCACAGAGTGGTGAGATCAGAAAGGAGGCCCCGAGGGATGAGACCAAGGCTGA
CACTGACACAGCCCCAGCTTCATTCCCTGCTCCTGGTCACTGTGAGAACTGTGGAATCAGCTTCTCAGGAGATGGCACCC
AAAGGCAGCAGCTCAAAATGTCGTGCAAAGACTGCCGAGCATGGAGAATTGCCTTTAACCGGGAACAGAGAATGTTTAAT
AGCCGAGGGTGTAGAGTATGCTGGGGCTGTCAGACCCAAGAGGACTGTGGCGGTTTCTGCATCTGCCTTCGCTCTCCGTG
CTTTGGTCTCAGGCGCCAGTGGAAATAGTCCAGCGACGTCGCCTACGGGGTAAACATGGCGGCCGCAGGGGAAACTGTGA
CGCCAACAAAGGTGGCTACTAGGCGGTGCCCCGGAGCCCGGCTACTGCCTCCACCTTCCTCTTCGCAGCCCACAGAGCTG
TACCGCAGAGCCCTGGGCCCTTGCCTCCTGGCGAGTTCATCTATTACTGTGTGGACGAGGACGAGCTACAGCCCTGCATG
AACCGCCGGCAGAACCGCAACTGCCAGGTCGCTCAGCCCGCTTACGGTGAATGGACTGTGTCCGCTGCGACTTCTGCTGC
AACAAGCCCACATTCGGGGGCAGCAACCAGAAGCTCCAGAAGTGTCACTGGCGCCAGTGCCTGCAGTTTGCCATGAAGCG
GCTGCTGCCCAGTGTCTGGTCAGAAGCTGAGGATGGGGCAGGATCACCCCCACCTTATGGCTGTCGAAAAAGGCCCAGCT
CTGCGTGACGGCACCATGTTGGCACTACCTTGAAGCCCAGCTTGGCTACTCCCACAGCCTAACCAGACCATACCCAGGCT
CCAAAGAAGCAGGCAGGAAGTAGATGGTGGCTTTGTGCTGCCCCCAGGCCCTGTTGCAGCTCACAGAAGCCCTGCTGCAG
GAGGCCCAGTGCTCTGACCT

Alignment

ORF - retro_cjac_1830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 68.71 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GDRIRSKVELTRYLGPACD--LTLFDFKQGILCYPAPKAHS-VAVTSKKRKKPSRP-SKTQKRQVGPQSG
          GDRIRSKVELTRYLG.A....LTLFD.KQGILCYPA.KAHS.VAV.SK...K...P..KT.K..VGPQSG
Retrocopy GDRIRSKVELTRYLGSAYHR*LTLFDGKQGILCYPAAKAHS<VAVASK-KGKKPSP<AKTRKCEVGPQSG

Parental  EVRKEAPKDETKADTVTVPASFPAPGCCENCGISFSGDGTQRQRLKTLCKDCRAQRIAFNREQRMFKSRG
          E.RKEAP.DETKADT.T.PASFPAPG.CENCGISFSGDGTQRQ.LK..CKDCRA.RIAFNREQRMF.SRG
Retrocopy EIRKEAPRDETKADTDTAPASFPAPGHCENCGISFSGDGTQRQQLKMSCKDCRAWRIAFNREQRMFNSRG

Parental  CGVCRGCQTQEDCGRCRICLRPPRPGLRRQWK-CVQRRCLRGKHGRRRGGCDSK-MAARRHPGAQPLPPP
          C.VC.GCQTQEDCG...ICLR.P..GLRRQWK..VQRR.LRGKHG.RRG.CD.....A.R......L.PP
Retrocopy CRVCWGCQTQEDCGGFCICLRSPCFGLRRQWK<IVQRRRLRGKHGGRRGNCDAN>KVATRRCPGARLLPP

Parental  PPSQSPEPTEPHPRALTPS-PPAEFIYYCVDEDELQPYTNRRQNRKCGAC-AACLRRMDCGRCDFCCDKP
          P...S..PTE...RAL.P..PP.EFIYYCVDEDELQP..NRRQNR.C.....A.LR.MDC.RCDFCC.KP
Retrocopy P--SSSQPTELYRRALGPC<PPGEFIYYCVDEDELQPCMNRRQNRNCQVA<SARLR*MDCVRCDFCCNKP

Parental  KFGGSNQKRQKCRWRQCLQFAMKRLLPSVWSESEDGAGSPPPYRRRKRPSSAQRHHLGPTLKPTLVTRTA
          .FGGSNQK.QKC.WRQCLQFAMKRLLPSVWSE.EDGAGSPPPY..RKRPSSA.RHH.G.TLKP.L.T.TA
Retrocopy TFGGSNQKLQKCHWRQCLQFAMKRLLPSVWSEAEDGAGSPPPYGCRKRPSSA*RHHVGTTLKPSLATPTA

Parental  RPDHTRAPSKQEAG-GGFVLPPPGTDLVFLREGASSPVQVP
          .PDHT.AP.KQ.....G....PPG.........A..PV..P
Retrocopy *PDHTQAPKKQAGS>DGGFVLPPGPVAAHRSPAAGGPVL*P

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	18.62 RPM
SRP051959_heart	0.00 RPM	19.96 RPM
SRP051959_kidney	0.00 RPM	24.87 RPM
SRP051959_liver	0.00 RPM	13.00 RPM
SRP051959_lung	0.00 RPM	27.20 RPM
SRP051959_lymph_node	0.00 RPM	33.88 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.83 RPM
SRP051959_spleen	0.00 RPM	30.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1830 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1830 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1830 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	ENSCJAG00000004959	1 retrocopy	retro_cjac_1830 ,
Monodelphis domestica	ENSMODG00000010534	1 retrocopy	retro_mdom_217,
Nomascus leucogenys	ENSNLEG00000011661	1 retrocopy	retro_nleu_3030,