RetrogeneDB ID: retro_cjac_4009

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL288040.1:3549..4298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCOR3
• Ensembl ID: ENSCJAG00000000282
• Aliases: None
• Description: REST corepressor 3 [Source:HGNC Symbol;Acc:25594]

Sequence

>retro_cjac_4009
GATGTTGGGATGAGAGTTGGAGCCGAATACCCAGCTCGGATCCCTGAATTTGATCCAGGTGCTACAAAGTACACAGATAA
AGACAGTGGAGGGATGTTTGTATGGTTTCCATATCACAGTATCCCAGATGCCAAACTGGATGAATACACTGCAATTGCAA
AGGAGAAGCATGGCTACGATGTGGAGCAGGCACTTGGCATGTTGTTCTGGCAGAAACGTGACGTTGAGAAGTCCCTTGCC
GGTCTCCCTAATTTCACTCCCTTTCCTGATGAGTGGACAGTGGAAGATAAAGTCCTATTTGAACAAGCCTTTAGCTTTCA
TGGAAACAGCTTTCACAGGATTCAGCAAATGCTTCCAGATAAGACAGTTGCAAGCCTTGCAAAATATTACTATTCCTAGA
AAAAAGCTCACTCTCGGACAAGTCTGATGGATCGCCAGGCTCGTAAACCAGCTAATAGACATACTCAGGGTGACCGTGAT
GATGATGTAGAAGAACCACATCCAACGGATGGGAACGATAGTGATTATGATCCCAAACAAGAGGGTAATACTGAACAACC
TGTTCTAACTAGCAAGATTGGACTCGGAAGAAGAGAGTATCAGAGTTTACAACATCGCCATCATTCTCAGCGTTCTAGTG
CCGTCCCCCTAAGGCCATGTGTTTAACCCAGGAAGATGTGGTAGCGGTTTCCTGTAGTCCCAATGCAGCCAACACCATTC
TGAGGCAACTGGACATGGAGCTGATCTCT

Alignment

ORF - retro_cjac_4009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.84 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DVGMRVGAEYQARIPEFDPGATKYTDKDNGGMLVWSPYHSIPDAKLDEYIAIAKEKHGYNVEQALGMLFW
          DVGMRVGAEY.ARIPEFDPGATKYTDKD.GGM.VW.PYHSIPDAKLDEY.AIAKEKHGY.VEQALGMLFW
Retrocopy DVGMRVGAEYPARIPEFDPGATKYTDKDSGGMFVWFPYHSIPDAKLDEYTAIAKEKHGYDVEQALGMLFW

Parental  HKHNIEKSLADLPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLPDKTIASLVKYYYSWKKTRSRT
          .K...EKSLA.LPNFTPFPDEWTVEDKVLFEQAFSFHG.SFHRIQQMLPDKT.ASL.KYYYS.KK..SRT
Retrocopy QKRDVEKSLAGLPNFTPFPDEWTVEDKVLFEQAFSFHGNSFHRIQQMLPDKTVASLAKYYYS*KKAHSRT

Parental  SLMDRQARKLANRHNQGDSDDDVEEPHPMDGNDSDYDPKKEAKKEGNTEQPVQTSKIGLGRREYQSLQHR
          SLMDRQARK.ANRH.QGD.DDDVEEPHP.DGNDSDYDPK.E....GNTEQPV.TSKIGLGRREYQSLQHR
Retrocopy SLMDRQARKPANRHTQGDRDDDVEEPHPTDGNDSDYDPKQE----GNTEQPVLTSKIGLGRREYQSLQHR

Parental  HHSQRSK-CRPPKGMYLTQEDVVAVSCSPNAANTILRQLDMELIS
          HHSQRS..CRPPK.M.LTQEDVVAVSCSPNAANTILRQLDMELIS
Retrocopy HHSQRSS<CRPPKAMCLTQEDVVAVSCSPNAANTILRQLDMELIS

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	0.60 RPM	5.92 RPM
SRP051959_heart	0.47 RPM	13.17 RPM
SRP051959_kidney	0.29 RPM	14.29 RPM
SRP051959_liver	0.43 RPM	4.07 RPM
SRP051959_lung	0.94 RPM	13.10 RPM
SRP051959_lymph_node	1.60 RPM	13.79 RPM
SRP051959_skeletal_muscle	0.50 RPM	13.12 RPM
SRP051959_spleen	0.59 RPM	12.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4009 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4009 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4009 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000282	3 retrocopies	retro_cjac_3349, retro_cjac_3915, retro_cjac_4009 ,