RetrogeneDB ID: retro_cjac_4093

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:78814760..78815617(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000010543
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DHDDS
• Ensembl ID: ENSCJAG00000009802
• Aliases: None
• Description: None

Sequence

>retro_cjac_4093
GAGCGGCAGGAAGGCCACTCACAGGGCTTCAACAAGCTAGCTGAGACCCTGGGGTGGTGTTTGAACCCGGGCATCCTAGA
GGTTACTGTCTACACATTCAACATTGAGAGCTTCAAATGCTCCAAGAGTAAGGTAGAAGGGCTTATGGATCTGGCCCGGC
AGAAGTTCAGCTGCTTGATGGAAGGAAACGAGAAAACGCAGAAGCATGAGTTGTGTATCTGGGTCCTGGGCGGTCTGCAC
TTGTTACCCTTGAATCTCCAGGAGCTGATTGCACAAGCTGTACAGGCCACGAAGAGCTGCAACAAGTCTTTCCTGAATGT
CTGTTTTGGATACACATTACGTCAGGAGATCAGCAATGCCAAGAGAGAGATGGCCTCGGGGGTGGAGCAAGGCCTGTTGG
ATCCCAGTGATATCTCTGATGAGTCCCTGCTTGGTAAGTGCCTCTATACCAACCACTCTCCTCATCCTGACATCTTGATG
CAGACTTCTGGAGAATTGCCACTGAATAACTTCTTGCTATGGCAGACCTCTTACTCCTGCCTGGTGTTCCAATACATTCT
GTCACCAAAATACACATTTTGGAACTTATTCGCGGCCATCCAGATGGGCCATAGCATGCTTCAGAAGGCCCGAGACATGT
ATGCAGAAGAGCGGGAGAGGCAGCAGCTGGAGAGGGACCAGGCTGCAGTGACAGAGCAGCTGCTGCAAGGAAGCTCCAAA
CCAGTGGGGACGCCCAGCTCCGAAGGACACACTTGCACAAACTCTCAATCAGACGGGAAGACCAAGTCCAAGGCTTCCTG
CAGGCCTCGGAATTCAAGCGAGCTGACTGGCTGGCATGTCTGGGCACTGCATCAGCC

Alignment

ORF - retro_cjac_4093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.38 %
• Parental protein coverage: 86.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERQEGHSQGFNKLAETLRWCLNLGILEVTVYAFSIENFKRSKSEVDGLMDLARQKFSRLMEEQEKLQKHG
          ERQEGHSQGFNKLAETL.WCLN.GILEVTVY.F.IE.FK.SKS.V.GLMDLARQKFS.LME..EK.QKH.
Retrocopy ERQEGHSQGFNKLAETLGWCLNPGILEVTVYTFNIESFKCSKSKVEGLMDLARQKFSCLMEGNEKTQKHE

Parental  VCIRVLGDLHLLPLDLQELIAQAVQATKNYNKCFLNVCFAYTSRHEISNAVREMAWGVEQGLLDPSDIS-
          .CI.VLG.LHLLPL.LQELIAQAVQATK..NK.FLNVCF.YT.R.EISNA.REMA.GVEQGLLDPSDIS.
Retrocopy LCIWVLGGLHLLPLNLQELIAQAVQATKSCNKSFLNVCFGYTLRQEISNAKREMASGVEQGLLDPSDISD

Parental  ESLLDKCLYTNRSPHPDILIRTSGEVRLSDFLLWQTSHSCLVFQPVLWPEYTFWNLFEAILQFQMNHSVL
          ESLL.KCLYTN.SPHPDIL..TSGE..L..FLLWQTS.SCLVFQ..L.P.YTFWNLF.AI...QM.HS.L
Retrocopy ESLLGKCLYTNHSPHPDILMQTSGELPLNNFLLWQTSYSCLVFQYILSPKYTFWNLFAAI---QMGHSML

Parental  QQKARDMYAEERKRQQLERDQATVTEQLLQ-EGLQASGDTQLRRTRLHKLSARREERVQGFLQALELKRA
          .QKARDMYAEER.RQQLERDQA.VTEQLLQ...LQ.SGD.QLRRT.LHKLS.RRE..VQGFLQA.E.KRA
Retrocopy -QKARDMYAEERERQQLERDQAAVTEQLLQ<RKLQTSGDAQLRRTHLHKLSIRREDQVQGFLQASEFKRA

Parental  DWLARLGTASA
          DWLA.LGTASA
Retrocopy DWLACLGTASA

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	8.34 RPM
SRP051959_heart	0.00 RPM	5.74 RPM
SRP051959_kidney	0.00 RPM	7.48 RPM
SRP051959_liver	0.00 RPM	7.88 RPM
SRP051959_lung	0.00 RPM	6.49 RPM
SRP051959_lymph_node	0.00 RPM	5.82 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.25 RPM
SRP051959_spleen	0.00 RPM	6.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4093 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4093 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	ENSCJAG00000009802	1 retrocopy	retro_cjac_4093 ,