RetrogeneDB ID: retro_cjac_403

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:68556384..68557189(+)
• Located in intron of: ENSCJAG00000009454

Retrocopy information

• Ensembl ID: ENSCJAG00000009459
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SVOPL
• Ensembl ID: ENSCJAG00000012965
• Aliases: None
• Description: None

Sequence

>retro_cjac_403
TTTTTGCCCACAAAATACCAAGGCTATATATTACCCTTGTCTCAGATGTTCTGGCTCATGGGCTCTCTGCTCATCATTGG
CCTGGCCTCTGTAATCATCCCCACCATCGGGTGGCGCTGGCTCATCCATGTCGCCTCCATCCCAGGCATCATCCTCATCA
TGGCCTTCAAGTTTATTCCTGAATCTGCCCAGTTTAATGTCTCCACTGGGAACACTCTGGCTGCCCTGGCCACTCTGGAG
TGCATCGCCAAGATGAACCACGTGGTCATGCCGGAGGGGAAGCTGGTGGAGCCTGTCCTGGAAAAAAAGAGGAACGTTTG
CAGACCTTTTGGATGCTAAATATTTACGGACCACATTACAGATCTGGGTCATATGGCTTGGAATCTCCTTTGCCTACTGC
AGGGTTATCTTGGGCAGTGCTGAGCTGCTGGAGCAGGACCTGGTCTGCGGTTCAAAGTCAGACTCTGAGGTGGTCGTGAC
TCAGGGGAACTCAGAGGAGAGCCAGAGCCCCTGCCACTGCCACATGTTTGCACCCACTGACTATCAGACCATAATCATCA
GCATTGTTAATGAAATTGCTCTGAATCCTTTAAATATCCCGGGCATCAATTTCCTGAAAAGACAGCTGAGCCTTTCCATT
ACCATGGGATGCACGGCTTTATTCTTCCTTCTCCTTAACATTTGCACATCAAGTGCCAGCCTGATTGGCTTCCCCTTTGT
GCTGAGGGCTCTGGTTTCTGCAAACTTCAACACCATCCACATTCACACAGCTGAGGTCTACCCCACCATGATGTGCACTT
TGGGG

Alignment

ORF - retro_cjac_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.01 %
• Parental protein coverage: 62.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FFPKEYRFWGLLSPQVFWLAGSLLIIGLASVIIPTIGWRWLIRVASIPGIILIMAFKFIPESARFNVSTG
          F.P..Y....L...Q.FWL.GSLLIIGLASVIIPTIGWRWLI.VASIPGIILIMAFKFIPESA.FNVSTG
Retrocopy FLPTKYQGYILPLSQMFWLMGSLLIIGLASVIIPTIGWRWLIHVASIPGIILIMAFKFIPESAQFNVSTG

Parental  NTPAALATLEHIAKMNRAVMPEGKLVEPILEK-RGRFADLLDAKYLRTTLQIWVIWLGISFAYYGVILAS
          NT.AALATLE.IAKMN..VMPEGKLVEP.LEK.RG.FADLLDAKYLRTTLQIWVIWLGISFAY..VIL.S
Retrocopy NTLAALATLECIAKMNHVVMPEGKLVEPVLEK>RGTFADLLDAKYLRTTLQIWVIWLGISFAYCRVILGS

Parental  AELLERDLVCGSKSDSEVVVTQGDSEESQSPCHCHMFAPSDYRTMIISTVGEIALNPLNILGINFLGRRL
          AELLE.DLVCGSKSDSEVVVTQG.SEESQSPCHCHMFAP.DY.T.IIS.V.EIALNPLNI.GINFL.R.L
Retrocopy AELLEQDLVCGSKSDSEVVVTQGNSEESQSPCHCHMFAPTDYQTIIISIVNEIALNPLNIPGINFLKRQL

Parental  SLSITMGCTALFFLLLNICTSSAGLIGFLFLLRALVAANFNTIYIYTAEVYPTTMRALG
          SLSITMGCTALFFLLLNICTSSA.LIGF.F.LRALV.ANFNTI.I.TAEVYPT.M..LG
Retrocopy SLSITMGCTALFFLLLNICTSSASLIGFPFVLRALVSANFNTIHIHTAEVYPTMMCTLG

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	0.09 RPM	2.09 RPM
SRP051959_heart	0.11 RPM	0.02 RPM
SRP051959_kidney	0.24 RPM	1.40 RPM
SRP051959_liver	0.26 RPM	0.02 RPM
SRP051959_lung	1.20 RPM	0.80 RPM
SRP051959_lymph_node	1.89 RPM	0.07 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.00 RPM
SRP051959_spleen	2.10 RPM	0.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_403 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_403 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012965	1 retrocopy	retro_cjac_403 ,
Dasypus novemcinctus	ENSDNOG00000006558	2 retrocopies	retro_dnov_594, retro_dnov_904,