RetrogeneDB ID: retro_cjac_3915

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286236.1:30521..31269(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007976
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_3915
GATGTTGAGATGAGAGTTGGAGCTGAATACCAAGCTCGGATCCCTGAATTTGATCCAGGTGCTACAAAGTACACAGATAA
AGACAGTGGAGGGATGTTTGTATGGTCTCCATATCACAGTATCCCGGATGCCAAACTGGATGAATACACTGCAATTGCAA
AGGAGAAGCATGGCTACGATGTGGAGCAGGCACTTGGCATGTTGTTCTGGCAGAAACATGACATTGAGAAGTCCCTTGCC
GGTCTCCCTAATTTCACTCCCTTTCCTGATGAGTGGACAGTGGAAGATAAAGTCCTATTTGAACAAGCCTTTAGCTTTCA
TGGAAAGAGCTTTCACAGGATTCAGCAAATGCTTCCAGGTAAGACAGTTGCAAGCCTTGAAAATATTACTATTCCTGGGA
AAAAGCTCACTCTCGGACAAGTCTGATGGATCGCCAGGCTCGTAAACCAGCTAATAGACATACTCAGGGTGACCGTGATG
ATGATGTAGAAGAACCACATCCAACGGATGGGAACGATAGTGATTATGATCCCAAACAAGAGGGTAATACTGAACAACCT
GTTCTAACTAGCAAGATTGGACTCGGAAGAAGAGAGTATCAGAGTTTACAACATCGCCATCATTCTCAGCGTTCTAGTGC
CGTCCCCCTAAGGGCATGTGTTTAACCCAGGAAGATGTGGTAGCGGTTTCCTGTAGTCCCAATGCAGCCAACACCATTCT
GAGGCAACTAGACGTGGAGCTGATCTCT

Alignment

ORF - retro_cjac_3915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.67 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DVGMRVGAEYQARIPEFDPGATKYTDKDNGGMLVWSPYHSIPDAKLDEYIAIAKEKHGYNVEQALGMLFW
          DV.MRVGAEYQARIPEFDPGATKYTDKD.GGM.VWSPYHSIPDAKLDEY.AIAKEKHGY.VEQALGMLFW
Retrocopy DVEMRVGAEYQARIPEFDPGATKYTDKDSGGMFVWSPYHSIPDAKLDEYTAIAKEKHGYDVEQALGMLFW

Parental  HKHNIEKSLADLPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLPDKTIASLV-KYYYSWKKTRSR
          .KH.IEKSLA.LPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLP.KT.ASL..KYYYSW.K..SR
Retrocopy QKHDIEKSLAGLPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLPGKTVASLE<KYYYSWEKAHSR

Parental  TSLMDRQARKLANRHNQGDSDDDVEEPHPMDGNDSDYDPKKEAKKEGNTEQPVQTSKIGLGRREYQSLQH
          TSLMDRQARK.ANRH.QGD.DDDVEEPHP.DGNDSDYDPK.E....GNTEQPV.TSKIGLGRREYQSLQH
Retrocopy TSLMDRQARKPANRHTQGDRDDDVEEPHPTDGNDSDYDPKQE----GNTEQPVLTSKIGLGRREYQSLQH

Parental  RHHSQRSK-CRPPKGMYLTQEDVVAVSCSPNAANTILRQLDMELIS
          RHHSQRS..CRPPKGM.LTQEDVVAVSCSPNAANTILRQLD.ELIS
Retrocopy RHHSQRSS<CRPPKGMCLTQEDVVAVSCSPNAANTILRQLDVELIS

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	0.38 RPM	5.92 RPM
SRP051959_heart	0.49 RPM	13.17 RPM
SRP051959_kidney	0.33 RPM	14.29 RPM
SRP051959_liver	0.43 RPM	4.07 RPM
SRP051959_lung	0.98 RPM	13.10 RPM
SRP051959_lymph_node	1.39 RPM	13.79 RPM
SRP051959_skeletal_muscle	0.31 RPM	13.12 RPM
SRP051959_spleen	0.44 RPM	12.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3915 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3915 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,