RetrogeneDB ID: retro_cjac_3349

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01170646.1:83869..84617(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007631
• 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_3349
GATGTTGGGATGAGAGTTGGAGCCGAATACCAAGCTCGGATCCCTGAATTTGATCCAGGTGCTACAAAGTACACAGATAA
AGACAGTGGAGGGATGTTTGTATGGTCTCCATATCACAGTATCCCAGATGCCAAACTGGATGAACACACTGCAATTGCAA
AGGAGAAGCATGGCTACGATGTGGAGCAGGCACTTGGCATGTTGTTCTGGCAGAAACATGACATTGAGAAGTCCCTTGCC
GGTCTCCCTAATTTCACTCCCTTTCCTGATGAGTGGACAGTGGAAGATAAAGTCCTATTTGAACAAGCCTTTAGCTTTCA
TGGAAAGAGCTTTCACAGGATTCAGCAAATGCTTCCAGATAAGACAGTTGCAAGCCTTGCAAATATTACTATTCCTGGGA
AAAAGCTCACTCTCGGACAAGTCTGATGGATCGCCAGGCTCGTAAACCAGCTAATAGACATACTCAGGGTGACAGTGATG
ATGATGTAGAAGAACCACATCCAACGGATGGGAACGATGGTGATTATGATCCCAAACAAGAGGGTAATACTGAACAACCT
GTCCAAACTAGCAAGATTGGACTCGGAAGAAGAGAGTATCAGAGTTTACAACATCGCCATCATTCTCAGCGTTCTAGTGC
CGTCCCCCTAAGGGCATGTGTTTAACCCAGGAAGATGTGGTAGCGGTTTCCTGTAGTCCCAATGCAGCCAACACCATTCT
GAGGCAACTGGACATGGAGCTGATCTCT

Alignment

ORF - retro_cjac_3349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.84 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DVGMRVGAEYQARIPEFDPGATKYTDKDNGGMLVWSPYHSIPDAKLDEYIAIAKEKHGYNVEQALGMLFW
          DVGMRVGAEYQARIPEFDPGATKYTDKD.GGM.VWSPYHSIPDAKLDE..AIAKEKHGY.VEQALGMLFW
Retrocopy DVGMRVGAEYQARIPEFDPGATKYTDKDSGGMFVWSPYHSIPDAKLDEHTAIAKEKHGYDVEQALGMLFW

Parental  HKHNIEKSLADLPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLPDKTIASLV-KYYYSWKKTRSR
          .KH.IEKSLA.LPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLPDKT.ASL..KYYYSW.K..SR
Retrocopy QKHDIEKSLAGLPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLPDKTVASLA<KYYYSWEKAHSR

Parental  TSLMDRQARKLANRHNQGDSDDDVEEPHPMDGNDSDYDPKKEAKKEGNTEQPVQTSKIGLGRREYQSLQH
          TSLMDRQARK.ANRH.QGDSDDDVEEPHP.DGND.DYDPK.E....GNTEQPVQTSKIGLGRREYQSLQH
Retrocopy TSLMDRQARKPANRHTQGDSDDDVEEPHPTDGNDGDYDPKQE----GNTEQPVQTSKIGLGRREYQSLQH

Parental  RHHSQRSK-CRPPKGMYLTQEDVVAVSCSPNAANTILRQLDMELIS
          RHHSQRS..CRPPKGM.LTQEDVVAVSCSPNAANTILRQLDMELIS
Retrocopy RHHSQRSS<CRPPKGMCLTQEDVVAVSCSPNAANTILRQLDMELIS

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	0.51 RPM	5.92 RPM
SRP051959_heart	0.51 RPM	13.17 RPM
SRP051959_kidney	0.09 RPM	14.29 RPM
SRP051959_liver	0.54 RPM	4.07 RPM
SRP051959_lung	0.76 RPM	13.10 RPM
SRP051959_lymph_node	1.00 RPM	13.79 RPM
SRP051959_skeletal_muscle	0.26 RPM	13.12 RPM
SRP051959_spleen	0.50 RPM	12.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3349 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3349 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3349 has 0 orthologous retrocopies within eutheria group .

---

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,