RetrogeneDB ID: retro_cjac_3169

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:115479240..115479902(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000016429
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KCTD18
• Ensembl ID: ENSCJAG00000031173
• Aliases: None
• Description: potassium channel tetramerization domain containing 18 [Source:HGNC Symbol;Acc:26446]

Sequence

>retro_cjac_3169
ATGGAAGGCCACGAGGCAGAAGAAGAGGTGCTAGATATTCTCCGACTGAATGTGGGTGGCTGTGTTTACACAGCCCGGCG
GGAGTCCTTGTGCCGCTTTAAGGACTCCATGTTGGCATCTATGTTCAGTGGTCGCTTTCCTCTAAAAACAGATGAGTCAG
GGGCTTGTGTTATTGACCGTGATGGACGTCTATTTAAATACCTTTTGGATTACCTTCATGGAGAAGTTCAGATTCCCACA
GATGAGCAAACCCGCATTGCCCTACAGGAAGAGGCTGATTACTTTGGCATCCCTTATCCGTATAGCCTGTCAGACCACTT
GGCCAATGAAATGGAGACATATTCTTTAAGGTCAAATATAGAACTTAAAAAGGCTTTAACAGACTTCTGTGATTCATATG
GCTTGGTCTGCAATAAACCAACAGTTTGGGTTCTCCACTATCTTAACACATCTGGTGCAAGCTGTGAGAGTAGAATTATT
GGTGTGTATGCCACAAAAAATGATGGAACAGATGCTATTGATAAGCAGCTGGGAGGAAGAATTCACAGCAAAAGCATTTT
TAAAAGAGAGGCAGGAAATAATGTACAGTACATTTGGAGCTATTATTCAGTAGCAAAGTTGAAGAAAAGATGGATGCCTT
TGATGCTTGGGAAGGAAAAGGT

Alignment

ORF - retro_cjac_3169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.65 %
• Parental protein coverage: 99.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGHEAEEEVLDILRLNVGGCVYTARRESLCRFKDSMLASMFSGRFPLKTDESGACVIDRDGRLFKYLLD
          MEGHEAEEEVLDILRLNVGGCVYTARRESLCRFKDSMLASMFSGRFPLKTDESGACVIDRDGRLFKYLLD
Retrocopy MEGHEAEEEVLDILRLNVGGCVYTARRESLCRFKDSMLASMFSGRFPLKTDESGACVIDRDGRLFKYLLD

Parental  YLHGEVQIPTDEQTRIALQEEADYFGIPYPYSLSDHLANEMETYSLRSNIELKKALTDFCDSYGLVCNKP
          YLHGEVQIPTDEQTRIALQEEADYFGIPYPYSLSDHLANEMETYSLRSNIELKKALTDFCDSYGLVCNKP
Retrocopy YLHGEVQIPTDEQTRIALQEEADYFGIPYPYSLSDHLANEMETYSLRSNIELKKALTDFCDSYGLVCNKP

Parental  TVWVLHYLNTSGASCESRIIGVYATKNDGTDAIDKQLGGRIHSKSIFKREAGNNVQYIWSYYSVAELKK-
          TVWVLHYLNTSGASCESRIIGVYATKNDGTDAIDKQLGGRIHSKSIFKREAGNNVQYIWSYYSVA.LKK.
Retrocopy TVWVLHYLNTSGASCESRIIGVYATKNDGTDAIDKQLGGRIHSKSIFKREAGNNVQYIWSYYSVAKLKK<

Parental  MMDAFDAWEGKG
          .MDAFDAWEGKG
Retrocopy KMDAFDAWEGKG

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	0.42 RPM	1.62 RPM
SRP051959_heart	0.44 RPM	1.07 RPM
SRP051959_kidney	0.51 RPM	1.24 RPM
SRP051959_liver	0.19 RPM	1.10 RPM
SRP051959_lung	0.63 RPM	1.92 RPM
SRP051959_lymph_node	0.43 RPM	2.33 RPM
SRP051959_skeletal_muscle	0.22 RPM	0.48 RPM
SRP051959_spleen	0.53 RPM	1.62 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3169 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3169 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000031173	2 retrocopies	retro_cjac_1956, retro_cjac_3169 ,
Otolemur garnettii	ENSOGAG00000012335	1 retrocopy	retro_ogar_3268,
Tarsius syrichta	ENSTSYG00000008420	2 retrocopies	retro_tsyr_293, retro_tsyr_896,