RetrogeneDB ID: retro_cjac_522

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:43921904..43922656(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032991
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WDR74
• Ensembl ID: ENSCJAG00000018581
• Aliases: None
• Description: None

Sequence

>retro_cjac_522
AGGATGCGCCAAGACCCAGCCCACCCCCATATGGTTGCCACAGGTGGGAAAGAGAATGCCTTGAAGATGTGGGACCTGCA
GGGCTCTGAGGAACCTGTGTTTAGGGCCAAGAACGTGCGGAATGACTGGCTAGACCTGCGAGTTCCCATCTGGGACCAGG
GCATACAGTTTCTCCCAGGATCACATAAGCTTGTCACCTGTGCAGGGTACCACCAGATTCGTGTCTATGATCCAGCCTCC
CCTCAGCGCTGGCCAGTCCTAGAGACCACCTATGGAGAGTACCCACTGACAGCTATGACCCTCACTCCTGGAGGCAACTC
AGTGATTGTGGGAAACATTCATGGGCAGCTGGCAGAAATTGACCTTCGGCAAGGGCGTCTACTGGGCTGTCTGAAGGGGC
TGGCAGGCAGCGTCTGTGGGTTGCAGTGCCACCCTTCCAAGCCTCTACTAGCCTCCTGTGGCTTGGACAGAGTCTTGAGG
ATACACAGGATCCAGAATCCACGGGGTCTGGCACATAAGGTTTATCTCAAGTCTCAATTGAACTGCCTCCTCCTGTCAGA
CAGGGACAACTGGGAGGATGAGTCCCAAGAACCTCAAGAACCCAACAACGTGCCCCTAGAAGACACAGAGACAGATGAAC
TTTGGGCATCCTTGGAGGCAGCTGCCAAGCAGAAGCTTCGGATTTGGAGCAGACCCAAGGAGCTCTCCAAACCAGGCGGA
GAAAGAAGAAGTGGCCTGGGTCCACCAGCCCC

Alignment

ORF - retro_cjac_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.84 %
• Parental protein coverage: 65.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RMRQDPAHPHVVATGGKENALKMWDLQGSEEPVFRAKNVRNDWLDLRVPIWDQDIQFLPGSQKLVTCTGY
          RMRQDPAHPH.VATGGKENALKMWDLQGSEEPVFRAKNVRNDWLDLRVPIWDQ.IQFLPGS.KLVTC.GY
Retrocopy RMRQDPAHPHMVATGGKENALKMWDLQGSEEPVFRAKNVRNDWLDLRVPIWDQGIQFLPGSHKLVTCAGY

Parental  HQVRVYDPASPQRRPVLETTYGEYPLTAMTLTPGGNSVIVGNTHGQLAEIDLRQGRLLGCLKGLAGSVRG
          HQ.RVYDPASPQR.PVLETTYGEYPLTAMTLTPGGNSVIVGN.HGQLAEIDLRQGRLLGCLKGLAGSV.G
Retrocopy HQIRVYDPASPQRWPVLETTYGEYPLTAMTLTPGGNSVIVGNIHGQLAEIDLRQGRLLGCLKGLAGSVCG

Parental  LQCHPSKPLLASCGLDRVLRIHRIQNPRGLEHKVYLKSQLNCLLLSDRDNWEDEPQEPQEPNNVPLEDTE
          LQCHPSKPLLASCGLDRVLRIHRIQNPRGL.HKVYLKSQLNCLLLSDRDNWEDE.QEPQEPNNVPLEDTE
Retrocopy LQCHPSKPLLASCGLDRVLRIHRIQNPRGLAHKVYLKSQLNCLLLSDRDNWEDESQEPQEPNNVPLEDTE

Parental  TDELWASLEAAAKRKL-SDLEQTQGALQTRRRKKKRPGSTSP
          TDELWASLEAAAK.KL.SDLEQTQGALQTRRRKKK.PGSTSP
Retrocopy TDELWASLEAAAKQKL<SDLEQTQGALQTRRRKKKWPGSTSP

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	4.81 RPM
SRP051959_heart	0.02 RPM	6.61 RPM
SRP051959_kidney	0.02 RPM	6.12 RPM
SRP051959_liver	0.00 RPM	6.11 RPM
SRP051959_lung	0.02 RPM	6.86 RPM
SRP051959_lymph_node	0.00 RPM	8.58 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.85 RPM
SRP051959_spleen	0.00 RPM	7.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_522 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_522 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018581	1 retrocopy	retro_cjac_522 ,